3rd iteration: try to find module that extends $MODULEPATH with '/Core' => '/Core' is in top_paths, so stop recursion PARAMETER DESCRIPTION top_paths
Prepend given module path to list of module paths, or bump it to 1st place.
PARAMETER DESCRIPTION Purge loaded modules.
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.ModulesTool.read_module_file","title":"Read module file with specified name.
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.ModulesTool.remove_module_path","title":"Remove specified module path (using 'module unuse').
PARAMETER DESCRIPTION Run module command.
PARAMETER DESCRIPTION list of arguments for module command; first argument should be the subcommand to run
dictionary with options that control certain aspects of how to run the module command
Set mod_paths, based on $MODULEPATH unless a list of module paths is specified.
PARAMETER DESCRIPTION Set path environment variable to the given list of paths.
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.ModulesTool.show","title":"Run 'module show' for the specified module.
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.ModulesTool.unload","title":"Unload all requested modules.
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.ModulesTool.unuse","title":"Remove module path via 'module unuse'.
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.ModulesTool.update","title":"Update after new modules were added.
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.ModulesTool.use","title":"Add path to $MODULEPATH via 'module use'.
PARAMETER DESCRIPTION Class that mock the module behaviour, used for operation not requiring modules. Eg. tests, fetch only
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.NoModulesTool.available","title":"Return all known modules tools.
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.curr_module_paths","title":"Return a list of current module paths.
PARAMETER DESCRIPTION Find library subdirectories for the specified software package.
Returns the library subdirectory, relative to software root. It fails if multiple library subdirs are found, unless only_one is False which yields a list of all library subdirs. If only_one is True and fs is None, select the one subdirectory with shared or static libraries, if possible.
PARAMETER DESCRIPTION Return the software root set for a particular software name.
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.get_software_root_env_var_name","title":"Return name of environment variable for software root.
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.get_software_version","title":"Return the software version set for a particular software name.
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.get_software_version_env_var_name","title":"Return name of environment variable for software root.
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.invalidate_module_caches_for","title":"Invalidate cache entries related to specified path.
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.mk_module_path","title":"Create a string representing the list of module paths.
","boost":0.5},{"location":"api/easybuild/tools/modules/#easybuild.tools.modules.modules_tool","title":"Reset module caches.
","boost":0.5},{"location":"api/easybuild/tools/multidiff/","title":"multidiff","text":"Class representing a multi-diff.
","boost":0.5},{"location":"api/easybuild/tools/multidiff/#easybuild.tools.multidiff.MultiDiff.__init__","title":"Create colored version of given line, with given color, if color mode is enabled.
","boost":0.5},{"location":"api/easybuild/tools/multidiff/#easybuild.tools.multidiff.MultiDiff.colorize","title":"Add colors to the diff line based on the squigly line.
","boost":0.5},{"location":"api/easybuild/tools/multidiff/#easybuild.tools.multidiff.MultiDiff.get_line","title":"Combine two squigly lines into a single squigly line.
","boost":0.5},{"location":"api/easybuild/tools/multidiff/#easybuild.tools.multidiff.MultiDiff.parse_line","title":"Generate a diff for multiple files, all compared to base.
PARAMETER DESCRIPTION Constructor.
","boost":0.5},{"location":"api/easybuild/tools/options/#easybuild.tools.options.EasyBuildOptions.avail_list","title":"Show list of available values passed by argument.
","boost":0.5},{"location":"api/easybuild/tools/options/#easybuild.tools.options.EasyBuildOptions.avail_repositories","title":"Show list of known repository types.
","boost":0.5},{"location":"api/easybuild/tools/options/#easybuild.tools.options.EasyBuildOptions.basic_options","title":"Get path value of configuration option as absolute path.
","boost":0.5},{"location":"api/easybuild/tools/options/#easybuild.tools.options.EasyBuildOptions.github_options","title":"GitHub integration configuration options.
","boost":0.5},{"location":"api/easybuild/tools/options/#easybuild.tools.options.EasyBuildOptions.job_options","title":"Option related to --job.
","boost":0.5},{"location":"api/easybuild/tools/options/#easybuild.tools.options.EasyBuildOptions.postprocess","title":"Regression test configuration options.
","boost":0.5},{"location":"api/easybuild/tools/options/#easybuild.tools.options.EasyBuildOptions.show_config","title":"Show specified EasyBuild configuration, relative to default EasyBuild configuration.
","boost":0.5},{"location":"api/easybuild/tools/options/#easybuild.tools.options.EasyBuildOptions.show_default_configfiles","title":"Show list of default config files.
","boost":0.5},{"location":"api/easybuild/tools/options/#easybuild.tools.options.EasyBuildOptions.show_default_moduleclasses","title":"Show list of default moduleclasses and description.
","boost":0.5},{"location":"api/easybuild/tools/options/#easybuild.tools.options.EasyBuildOptions.show_system_info","title":"Show system information.
","boost":0.5},{"location":"api/easybuild/tools/options/#easybuild.tools.options.EasyBuildOptions.validate","title":"Check configuration options, some combinations are not allowed.
","boost":0.5},{"location":"api/easybuild/tools/options/#easybuild.tools.options.check_root_usage","title":"Clean up temporary directory and exit.
PARAMETER DESCRIPTION Convert a dictionary with configuration option values to command-line options for the 'eb' command. Can by used to convert e.g. easyconfig-specific options from an easystack file to a list of strings that can be fed into the EasyBuild option parser
PARAMETER DESCRIPTION Parse metadata for external modules.
PARAMETER DESCRIPTION list of (glob patterns for) paths to config files providing metadata for external modules
Pretty print options dict.
PARAMETER DESCRIPTION Create a dictionary with specified software build options. The options arguments should be a parsed option list (as delivered by parse_options(args).options)
","boost":0.5},{"location":"api/easybuild/tools/options/#easybuild.tools.options.set_tmpdir","title":"Set temporary directory to be used by tempfile and others.
","boost":0.5},{"location":"api/easybuild/tools/options/#easybuild.tools.options.set_up_configuration","title":"Set up EasyBuild configuration, by parsing configuration settings & initialising build options.
PARAMETER DESCRIPTION command line arguments to take into account when parsing the EasyBuild configuration settings
reconfigure singletons that hold configuration dictionaries. Use with care: normally, configuration shouldn't be changed during a run. Exceptions are when looping over items in EasyStack files
Tools for controlling output to terminal produced by EasyBuild.
Dummy shim for Rich classes. Used in case Rich is not available, or when EasyBuild is not configured to use rich output style.
","boost":0.5},{"location":"api/easybuild/tools/output/#easybuild.tools.output.colorize","title":"Colorize given text, with specified color.
","boost":0.5},{"location":"api/easybuild/tools/output/#easybuild.tools.output.download_all_progress_bar","title":"Get progress bar to show progress on downloading of all source files.
","boost":0.5},{"location":"api/easybuild/tools/output/#easybuild.tools.output.download_one_progress_bar","title":"Get progress bar to show progress for downloading a file of known size.
","boost":0.5},{"location":"api/easybuild/tools/output/#easybuild.tools.output.download_one_progress_bar_unknown_size","title":"Get progress bar to show progress for downloading a file of unknown size.
","boost":0.5},{"location":"api/easybuild/tools/output/#easybuild.tools.output.easyconfig_progress_bar","title":"Get progress bar to display progress for installing a single easyconfig file.
","boost":0.5},{"location":"api/easybuild/tools/output/#easybuild.tools.output.extensions_progress_bar","title":"Get progress bar to show progress for installing extensions.
","boost":0.5},{"location":"api/easybuild/tools/output/#easybuild.tools.output.get_progress_bar","title":"Get progress bar of given type.
","boost":0.5},{"location":"api/easybuild/tools/output/#easybuild.tools.output.print_checks","title":"Print overview of checks that were made.
","boost":0.5},{"location":"api/easybuild/tools/output/#easybuild.tools.output.progress_bar_cache","title":"Function decorator to cache created progress bars for easy retrieval.
","boost":0.5},{"location":"api/easybuild/tools/output/#easybuild.tools.output.rich_live_cm","title":"Return Live instance to use as context manager.
","boost":0.5},{"location":"api/easybuild/tools/output/#easybuild.tools.output.show_progress_bars","title":"Return whether or not to show progress bars.
","boost":0.5},{"location":"api/easybuild/tools/output/#easybuild.tools.output.start_progress_bar","title":"Start progress bar of given type.
PARAMETER DESCRIPTION Get progress bar to display overall progress.
","boost":0.5},{"location":"api/easybuild/tools/output/#easybuild.tools.output.stop_progress_bar","title":"Stop progress bar of given type.
","boost":0.5},{"location":"api/easybuild/tools/output/#easybuild.tools.output.update_progress_bar","title":"Update progress bar of given type (if it was started), add progress of given size.
PARAMETER DESCRIPTION Return whether or not to use Rich to produce rich output.
","boost":0.5},{"location":"api/easybuild/tools/parallelbuild/","title":"parallelbuild","text":"Module for doing parallel builds. This uses a PBS-like cluster. You should be able to submit jobs (which can have dependencies)
Support for PBS is provided via the PbsJob class. If you want you could create other job classes and use them here.
Build easyconfigs in parallel by submitting jobs to a batch-queuing system. Return list of jobs submitted.
Creates a job to build a single easyconfig.
PARAMETER DESCRIPTION format string for command, full path to an easyconfig file will be substituted in it
optional output path; --regtest-output-dir will be used inside the job with this variable returns the job
Submit jobs.
PARAMETER DESCRIPTION Dependency resolution functionality, a.k.a. robot.
Check for conflicts in dependency graphs for specified easyconfigs.
PARAMETER DESCRIPTION Determine robot path.
","boost":0.5},{"location":"api/easybuild/tools/robot/#easybuild.tools.robot.dry_run","title":"Compose dry run overview for supplied easyconfigs: * [ ] for unavailable * [x] for available * [F] for forced * [R] for rebuild
PARAMETER DESCRIPTION Determine subset of easyconfigs for which no module is installed yet.
","boost":0.5},{"location":"api/easybuild/tools/robot/#easybuild.tools.robot.raise_error_missing_deps","title":"Raise error to report missing dependencies.
","boost":0.5},{"location":"api/easybuild/tools/robot/#easybuild.tools.robot.resolve_dependencies","title":"boolean indicating whether all dependencies must be retained, regardless of availability; retain all deps when True, check matching build option when False
Search for easyconfigs, if a query is provided.
PARAMETER DESCRIPTION Tools to run commands.
Check status of command that was started asynchronously.
:result: dict value with result of the check (boolean 'done', 'exit_code', 'output')
PARAMETER DESCRIPTION List of: regular expressions (as strings) to error on, or tuple of regular expression and action (any of [IGNORE, WARN, ERROR])
Complete running of command represented by passed subprocess.Popen instance.
PARAMETER DESCRIPTION if True, just return True/False to indicate success, else return a tuple: (output, exit_code)
regex used to check the output for errors; if True it will use the default (see parse_log_for_error)
Check provided string (command output) for messages matching specified regular expressions, and return 2-tuple with list of warnings and errors.
PARAMETER DESCRIPTION List of: regular expressions (as strings) to error on, or tuple of regular expression and action (any of [IGNORE, WARN, ERROR])
Get output from running process (that was opened with subprocess.Popen).
PARAMETER DESCRIPTION Parse command output and construct return value.
PARAMETER DESCRIPTION if True, just return True/False to indicate success, else return a tuple: (output, exit_code)
regex used to check the output for errors; if True it will use the default (see parse_log_for_error)
txt is multiline string. - in memory regExp is a one-line regular expression - default
","boost":0.5},{"location":"api/easybuild/tools/run/#easybuild.tools.run.run_cmd","title":"if True, just return True/False to indicate success, else return a tuple: (output, exit_code)
regex used to check the output for errors; if True it will use the default (see parse_log_for_error)
indicate whether all output of command should be logged to a separate temporary logfile
allow commands to not run in a shell (especially useful for cmd lists), defaults to True
Function decorator to cache (and retrieve cached) results of running commands.
","boost":0.5},{"location":"api/easybuild/tools/run/#easybuild.tools.run.run_cmd_qa","title":"if True, just return True/False to indicate success, else return a tuple: (output, exit_code)
regex used to check the output for errors; if True it will use the default (see parse_log_for_error)
Check presence and version of required and optional EasyBuild dependencies, and report back to terminal.
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.check_linked_shared_libs","title":"Check for (lack of) patterns in linked shared libraries for binary/library at specified path. Uses 'ldd' on Linux and 'otool -L' on macOS to determine linked shared libraries.
Returns True or False for dynamically linked binaries and shared libraries to indicate whether all patterns match and antipatterns don't match.
Returns None if given path is not a dynamically linked binary or library.
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.check_os_dependency","title":"Check if dependency is available from OS.
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.check_python_version","title":"Check currently used Python version.
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.det_parallelism","title":"Determine level of parallelism that should be used. Default: educated guess based on # cores and 'ulimit -u' setting: min(# cores, ((ulimit -u) - 15) // 6)
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.det_pypkg_version","title":"Determine version of a Python package.
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.det_terminal_size","title":"Determine the current size of the terminal window.
RETURNS DESCRIPTION Search library by file name in the system Return absolute path to existing libraries
PARAMETER DESCRIPTION Determine CPU architecture name via archspec (if available).
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.get_cpu_architecture","title":"Determine CPU family.
RETURNS DESCRIPTION Returns the (maximum) cpu speed in MHz, as a float value. In case of throttling, the highest cpu speed is returns.
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.get_cpu_vendor","title":"Get raw output from command that reports linked libraries for dynamically linked executables/libraries, or None for other types of files.
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.get_os_name","title":"Determine system name, e.g., 'redhat' (generic), 'centos', 'debian', 'fedora', 'suse', 'ubuntu', 'red hat enterprise linux server', 'SL' (Scientific Linux), 'opensuse', ...
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.get_os_type","title":"Determine system type, e.g., 'Linux', 'Darwin', 'Java'.
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.get_os_version","title":"Determine system version.
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.get_platform_name","title":"Return a dictionary with system information.
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.get_tool_version","title":"Get output of running version option for specific command line tool. Output is returned as a single-line string (newlines are replaced by '; ').
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.get_total_memory","title":"Return absolute path to loaded library using dlinfo Based on https://stackoverflow.com/a/35683698
PARAMETER DESCRIPTION Pick the correct dependency version to use for this system. Input can either be: * a string value (or None) * a dict with options to choose from
Return value is the version to use or False to skip this dependency.
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.pick_system_specific_value","title":"Descriptive string about the value to be retrieved. Used for logging.
Determine list of available cores for current process.
","boost":0.5},{"location":"api/easybuild/tools/systemtools/#easybuild.tools.systemtools.use_group","title":"Use group with specified name.
","boost":0.5},{"location":"api/easybuild/tools/testing/","title":"testing","text":"Module for doing parallel builds. This uses a PBS-like cluster. You should be able to submit jobs (which can have dependencies)
Support for PBS is provided via the PbsJob class. If you want you could create other job classes and use them here.
Create test report for easyconfigs PR, in Markdown format.
PARAMETER DESCRIPTION Post test report in a gist, and submit comment in easyconfigs or easyblocks PR.
","boost":0.5},{"location":"api/easybuild/tools/testing/#easybuild.tools.testing.regtest","title":"dictionary specifying build specifications (e.g. version, toolchain, ...)
Get session state: timestamp, dump of environment, system info.
","boost":0.5},{"location":"api/easybuild/tools/testing/#easybuild.tools.testing.upload_test_report_as_gist","title":"Upload test report as a gist.
","boost":0.5},{"location":"api/easybuild/tools/utilities/","title":"utilities","text":"Flatten a list of lists.
","boost":0.5},{"location":"api/easybuild/tools/utilities/#easybuild.tools.utilities.get_class_for","title":"Get class for a given Python class name and Python module path.
PARAMETER DESCRIPTION Get list of all subclasses, recursively from the specified base class.
","boost":0.5},{"location":"api/easybuild/tools/utilities/#easybuild.tools.utilities.get_subclasses_dict","title":"Get dict with subclasses per classes, recursively from the specified base class.
","boost":0.5},{"location":"api/easybuild/tools/utilities/#easybuild.tools.utilities.import_available_modules","title":"Import all available module in the specified namespace.
PARAMETER DESCRIPTION The namespace to import modules from.
Returns a MarkDown table with given titles and columns (a nested list of string columns for each column)
","boost":0.5},{"location":"api/easybuild/tools/utilities/#easybuild.tools.utilities.mk_rst_table","title":"Returns an rst table with given titles and columns (a nested list of string columns for each column)
","boost":0.5},{"location":"api/easybuild/tools/utilities/#easybuild.tools.utilities.natural_keys","title":"Can be used as the sort key in list.sort(key=natural_keys) to sort in natural order (i.e. respecting numbers)
","boost":0.5},{"location":"api/easybuild/tools/utilities/#easybuild.tools.utilities.nub","title":"Returns the unique items of a list of hashables, while preserving order of the original list, i.e. the first unique element encoutered is retained.
Code is taken from http://stackoverflow.com/questions/480214/how-do-you-remove-duplicates-from-a-list-in-python-whilst-preserving-order
Supposedly, this is one of the fastest ways to determine the unique elements of a list.
Decorator to guard functions/methods against missing required module with specified name.
","boost":0.5},{"location":"api/easybuild/tools/utilities/#easybuild.tools.utilities.quote_py_str","title":"Version of quote_str specific for generating use in Python context (e.g., easyconfig parameters).
","boost":0.5},{"location":"api/easybuild/tools/utilities/#easybuild.tools.utilities.quote_str","title":"Obtain a new value to be used in string replacement context.
For non-string values, it just returns the exact same value.
For string values, it tries to escape the string in quotes, e.g., foo becomes 'foo', foo'bar becomes \"foo'bar\", foo'bar\"baz becomes \"\"\"foo'bar\"baz\"\"\", etc.
PARAMETER DESCRIPTION All non-letter and non-numeral characters are considered unwanted except for underscore ('_').
","boost":0.5},{"location":"api/easybuild/tools/utilities/#easybuild.tools.utilities.shell_quote","title":"Wrap provided token in single quotes (to escape space and characters with special meaning in a shell), so it can be used in a shell command. This results in token that is not expanded/interpolated by the shell.
","boost":0.5},{"location":"api/easybuild/tools/utilities/#easybuild.tools.utilities.time2str","title":"Return string representing provided datetime.timedelta value in human-readable form.
","boost":0.5},{"location":"api/easybuild/tools/utilities/#easybuild.tools.utilities.trace_msg","title":"Print trace message.
","boost":0.5},{"location":"api/easybuild/tools/variables/","title":"variables","text":"Module that contains a set of classes and function to generate variables to be used e.g., in compiling or linking
Given prefix and list of paths, return first that exists if suffix : extend the paths with prefixes if filename : look for filename in prefix+paths
","boost":0.5},{"location":"api/easybuild/tools/variables/#easybuild.tools.variables.AbsPathList.append_subdirs","title":"Named extend, value is list type (TODO: tighten the allowed values) name not used anymore
","boost":0.5},{"location":"api/easybuild/tools/variables/#easybuild.tools.variables.ListOfLists.sanitize","title":"Class to hold variable-like key/value pairs All values are lists (or derived from list class) most only have a single element though some are lists of lists str creates a single string
Return the class associated with the name according to the DEFAULT_CLASS and MAP_CLASS
","boost":0.5},{"location":"api/easybuild/tools/variables/#easybuild.tools.variables.Variables.get_instance","title":"Return the class associated with the name according to the DEFAULT_LISTCLASS and MAP_LISTCLASS
","boost":0.5},{"location":"api/easybuild/tools/variables/#easybuild.tools.variables.Variables.join","title":"Join all values in others into name it is first tested if other is an existing element else it is nappend-ed
","boost":0.5},{"location":"api/easybuild/tools/variables/#easybuild.tools.variables.Variables.try_function_on_element","title":"Return class based on default map_class if key == str -> value = class else: key = class -> list of strings
","boost":0.5},{"location":"api/easybuild/tools/variables/#easybuild.tools.variables.join_map_class","title":"Module that takes control of versioning.
Returns the git revision (e.g. aab4afc016b742c6d4b157427e192942d0e131fe), or UNKNOWN is getting the git revision fails
Get Apptainer version.
","boost":0.5},{"location":"api/easybuild/tools/containers/apptainer/#easybuild.tools.containers.apptainer.ApptainerContainer.build_image","title":"Build container image by calling out to 'sudo apptainer build'.
","boost":0.5},{"location":"api/easybuild/tools/containers/base/","title":"base","text":"The parent class for concrete container recipe and image generator. Subclasses have to provide at least template resolution and image creation logic.
","boost":0.5},{"location":"api/easybuild/tools/containers/base/#easybuild.tools.containers.base.ContainerGenerator.build_image","title":"This method will be used on the concrete subclass to build the image using The path of the container recipe.
","boost":0.5},{"location":"api/easybuild/tools/containers/base/#easybuild.tools.containers.base.ContainerGenerator.generate","title":"The entry point for container recipe and image generation. It starts by validating the needed tools are available using TOOLS class attribute. If the validation passes, it will generate the container recipe, and optionally build out of it the container.
","boost":0.5},{"location":"api/easybuild/tools/containers/base/#easybuild.tools.containers.base.ContainerGenerator.generate_recipe","title":"This method will make use of resolve_template and resolve_template_data methods in order to generate the container recipe.
","boost":0.5},{"location":"api/easybuild/tools/containers/base/#easybuild.tools.containers.base.ContainerGenerator.resolve_template","title":"This method should be implemented by the concrete subclass to return the correct template for the container recipe.
","boost":0.5},{"location":"api/easybuild/tools/containers/base/#easybuild.tools.containers.base.ContainerGenerator.resolve_template_data","title":"This method should be implemented by the concrete subclass to return a dictionary of template data for container recipe generation.
","boost":0.5},{"location":"api/easybuild/tools/containers/base/#easybuild.tools.containers.base.ContainerGenerator.validate","title":"A method that should contain all the validation logic for both container recipe (Singularity, Dockerfile, ...) and image generation.
","boost":0.5},{"location":"api/easybuild/tools/containers/base/#easybuild.tools.containers.base.ContainerGenerator.validate_tools","title":"A method that gets called as part of image generation that uses TOOLS class attribute to check for the existence of the needed binary/tools on the host system.
","boost":0.5},{"location":"api/easybuild/tools/containers/common/","title":"common","text":"Return template container recipe.
","boost":0.5},{"location":"api/easybuild/tools/containers/docker/#easybuild.tools.containers.docker.DockerContainer.resolve_template_data","title":"Return template data for container recipe.
","boost":0.5},{"location":"api/easybuild/tools/containers/docker/#easybuild.tools.containers.docker.DockerContainer.validate","title":"Perform validation of specified container configuration.
","boost":0.5},{"location":"api/easybuild/tools/containers/singularity/","title":"singularity","text":"Support for generating singularity container recipes and creating container images
Build container image by calling out to 'sudo singularity build'.
","boost":0.5},{"location":"api/easybuild/tools/containers/singularity/#easybuild.tools.containers.singularity.SingularityContainer.resolve_template","title":"Return template container recipe.
","boost":0.5},{"location":"api/easybuild/tools/containers/singularity/#easybuild.tools.containers.singularity.SingularityContainer.resolve_template_data","title":"Return template data for container recipe.
","boost":0.5},{"location":"api/easybuild/tools/containers/singularity/#easybuild.tools.containers.singularity.SingularityContainer.resolve_template_data_config","title":"Return template data for container recipe based on what is passed to --container-config.
","boost":0.5},{"location":"api/easybuild/tools/containers/singularity/#easybuild.tools.containers.singularity.SingularityContainer.singularity_version","title":"Get Singularity version.
","boost":0.5},{"location":"api/easybuild/tools/containers/utils/","title":"utils","text":"This function is a predicate check for the existence of tool_name on the system PATH. If min_tool_version is not None, it will check that the version has an equal or higher value.
","boost":0.5},{"location":"api/easybuild/tools/containers/utils/#easybuild.tools.containers.utils.det_os_deps","title":"Using an easyconfigs object, this utility function will return a list of operating system dependencies that are required to build one or more easybuilds modules.
","boost":0.5},{"location":"api/easybuild/tools/job/","title":"job","text":"Abstract interface for submitting jobs and related utilities.
Constructor.
","boost":0.5},{"location":"api/easybuild/tools/job/backend/#easybuild.tools.job.backend.JobBackend.complete","title":"Complete a bulk job submission.
Initialise the job backend, to start a bulk job submission.
Add a job to the queue.
Return all known job execution backends.
","boost":0.5},{"location":"api/easybuild/tools/job/backend/#easybuild.tools.job.backend.job_backend","title":"Interface for submitting jobs via GC3Pie.
This is used to stop the build process in case some dependency fails. See also <https://github.com/easybuilders/easybuild-framework/issues/1441>_
","boost":0.5},{"location":"api/easybuild/tools/job/gc3pie/#easybuild.tools.job.gc3pie.GC3Pie","title":"Use the GC3Pie framework to submit and monitor compilation jobs, see http://gc3pie.readthedocs.org/.
In contrast with accessing an external service, GC3Pie implements its own workflow manager, which means eb --job --job-backend=GC3Pie will keep running until all jobs have terminated.
","boost":0.5},{"location":"api/easybuild/tools/job/gc3pie/#easybuild.tools.job.gc3pie.GC3Pie.__init__","title":"GC3Pie JobBackend constructor.
","boost":0.5},{"location":"api/easybuild/tools/job/gc3pie/#easybuild.tools.job.gc3pie.GC3Pie.complete","title":"Complete a bulk job submission.
Create engine, and progress it until all jobs have terminated.
","boost":0.5},{"location":"api/easybuild/tools/job/gc3pie/#easybuild.tools.job.gc3pie.GC3Pie.init","title":"Initialise the GC3Pie job backend.
","boost":0.5},{"location":"api/easybuild/tools/job/gc3pie/#easybuild.tools.job.gc3pie.GC3Pie.make_job","title":"Create and return a job object with the given parameters.
Argument script is the content of the job script itself, i.e., the sequence of shell commands that will be executed.
Argument name sets the job's human-readable name.
Optional argument env_vars is a dictionary with key-value pairs of environment variables that should be passed on to the job.
Optional arguments hours and cores should be integer values: - hours must be in the range 1 .. MAX_WALLTIME; - cores depends on which cluster the job is being run.
","boost":0.5},{"location":"api/easybuild/tools/job/gc3pie/#easybuild.tools.job.gc3pie.GC3Pie.queue","title":"Add a job to the queue, optionally specifying dependencies.
PARAMETER DESCRIPTION jobs on which this job depends.
Interface module to TORQUE (PBS).
create a new Job to be submitted to PBS env_vars is a dictionary with key-value pairs of environment variables that should be passed on to the job hours and cores should be integer values. hours can be 1 - (max walltime), cores depends on which cluster it is being run.
","boost":0.5},{"location":"api/easybuild/tools/job/pbs_python/#easybuild.tools.job.pbs_python.PbsJob.__str__","title":"Return the job ID as a string.
","boost":0.5},{"location":"api/easybuild/tools/job/pbs_python/#easybuild.tools.job.pbs_python.PbsJob.add_dependencies","title":"Add dependencies to this job.
Return whether this job has holds or not.
","boost":0.5},{"location":"api/easybuild/tools/job/pbs_python/#easybuild.tools.job.pbs_python.PbsJob.info","title":"Release hold on job of specified type.
","boost":0.5},{"location":"api/easybuild/tools/job/pbs_python/#easybuild.tools.job.pbs_python.PbsJob.remove","title":"Set hold on job of specified type.
","boost":0.5},{"location":"api/easybuild/tools/job/pbs_python/#easybuild.tools.job.pbs_python.PbsJob.state","title":"Return the state of the job State can be 'not submitted', 'running', 'queued' or 'finished',
","boost":0.5},{"location":"api/easybuild/tools/job/pbs_python/#easybuild.tools.job.pbs_python.PbsPython","title":"Constructor.
","boost":0.5},{"location":"api/easybuild/tools/job/pbs_python/#easybuild.tools.job.pbs_python.PbsPython.complete","title":"Complete a bulk job submission.
Release all user holds on submitted jobs, and disconnect from server.
","boost":0.5},{"location":"api/easybuild/tools/job/pbs_python/#easybuild.tools.job.pbs_python.PbsPython.connect_to_server","title":"Connect to PBS server, set and return connection.
","boost":0.5},{"location":"api/easybuild/tools/job/pbs_python/#easybuild.tools.job.pbs_python.PbsPython.disconnect_from_server","title":"Disconnect current connection.
","boost":0.5},{"location":"api/easybuild/tools/job/pbs_python/#easybuild.tools.job.pbs_python.PbsPython.init","title":"Initialise the job backend.
Connect to the PBS server & reset list of submitted jobs.
","boost":0.5},{"location":"api/easybuild/tools/job/pbs_python/#easybuild.tools.job.pbs_python.PbsPython.make_job","title":"Add a job to the queue.
PARAMETER DESCRIPTION jobs on which this job depends.
Constructor.
","boost":0.5},{"location":"api/easybuild/tools/job/slurm/#easybuild.tools.job.slurm.Slurm.complete","title":"Complete a bulk job submission.
Release all user holds on submitted jobs, and disconnect from server.
","boost":0.5},{"location":"api/easybuild/tools/job/slurm/#easybuild.tools.job.slurm.Slurm.init","title":"Initialise the PySlurm job backend.
","boost":0.5},{"location":"api/easybuild/tools/job/slurm/#easybuild.tools.job.slurm.Slurm.make_job","title":"Create and return a job dict with the given parameters.
","boost":0.5},{"location":"api/easybuild/tools/job/slurm/#easybuild.tools.job.slurm.Slurm.queue","title":"Add a job to the queue.
PARAMETER DESCRIPTION jobs on which this job depends.
Job class for SLURM jobs.
","boost":0.5},{"location":"api/easybuild/tools/job/slurm/#easybuild.tools.job.slurm.SlurmJob.__init__","title":"Create a new Job to be submitted to SLURM.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/","title":"module_naming_scheme","text":"Implementation of a hierarchical module naming scheme using module classes.
Class implementing an extended hierarchical module naming scheme using the 'moduleclass' easyconfig parameter to categorize modulefiles on each level of the hierarchy.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/categorized_hmns/#easybuild.tools.module_naming_scheme.categorized_hmns.CategorizedHMNS.categorize_paths","title":"Returns a list of paths where all known (valid) module classes have been added to each of the given base paths.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/categorized_hmns/#easybuild.tools.module_naming_scheme.categorized_hmns.CategorizedHMNS.det_init_modulepaths","title":"Determine list of initial module paths (i.e., top of the hierarchy). Appends all known (valid) module classes to the top-level base path.
Examples: Core/","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/categorized_hmns/#easybuild.tools.module_naming_scheme.categorized_hmns.CategorizedHMNS.det_modpath_extensions","title":"det_modpath_extensions(ec)","text":"
Determine module path extensions, if any. Appends all known (valid) module classes to the base path of the corresponding hierarchy level.
Examples: Compiler/GCC/4.8.3/ (for GCC/4.8.3 module), MPI/GCC/4.8.3/OpenMPI/1.6.5/ (for OpenMPI/1.6.5 module)","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/categorized_hmns/#easybuild.tools.module_naming_scheme.categorized_hmns.CategorizedHMNS.det_module_subdir","title":"det_module_subdir(ec)","text":"
Determine module subdirectory, relative to the top of the module path. This determines the separation between module names exposed to users, and what's part of the $MODULEPATH. This implementation appends the 'moduleclass' easyconfig parameter to the base path of the corresponding hierarchy level.
Determine user module path extensions, if any. As typical users are not expected to have many local modules, further categorizing them using module classes is considered overkill. Thus, we are using a plain hierarchical scheme for user modules instead.
Examples: Compiler/GCC/4.8.3 (for GCC/4.8.3 module), MPI/GCC/4.8.3/OpenMPI/1.6.5 (for OpenMPI/1.6.5 module)
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/categorized_mns/","title":"categorized_mns","text":"Implementation of a categorized module naming scheme using module classes.
Class implementing the categorized module naming scheme.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/categorized_mns/#easybuild.tools.module_naming_scheme.categorized_mns.CategorizedModuleNamingScheme.det_full_module_name","title":"Determine full module name from given easyconfig, according to the thematic module naming scheme.
PARAMETER DESCRIPTION dict-like object with easyconfig parameter values (e.g. 'name', 'version', etc.)
Determine whether the specified (short) module name is a module for software with the specified name. Default implementation checks via a strict regex pattern, and assumes short module names are of the form: /[-]","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/easybuild_mns/","title":"easybuild_mns","text":"
Implementation of (default) EasyBuild module naming scheme.
Class implementing the default EasyBuild module naming scheme.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/easybuild_mns/#easybuild.tools.module_naming_scheme.easybuild_mns.EasyBuildMNS.det_full_module_name","title":"Determine full module name from given easyconfig, according to the EasyBuild module naming scheme.
PARAMETER DESCRIPTION dict-like object with easyconfig parameter values (e.g. 'name', 'version', etc.)
string with full module name /, e.g.: 'gzip/1.5-goolf-1.4.10'","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/hierarchical_mns/","title":"hierarchical_mns","text":"
Implementation of an example hierarchical module naming scheme.
Class implementing an example hierarchical module naming scheme.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/hierarchical_mns/#easybuild.tools.module_naming_scheme.hierarchical_mns.HierarchicalMNS.det_full_module_name","title":"Determine full module name, relative to the top of the module path. Examples: Core/GCC/4.8.3, Compiler/GCC/4.8.3/OpenMPI/1.6.5, MPI/GCC/4.8.3/OpenMPI/1.6.5/HPL/2.1
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/hierarchical_mns/#easybuild.tools.module_naming_scheme.hierarchical_mns.HierarchicalMNS.det_full_version","title":"Determine full version, taking into account version prefix/suffix.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/hierarchical_mns/#easybuild.tools.module_naming_scheme.hierarchical_mns.HierarchicalMNS.det_init_modulepaths","title":"Determine list of initial module paths (i.e. top of the hierarchy).
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/hierarchical_mns/#easybuild.tools.module_naming_scheme.hierarchical_mns.HierarchicalMNS.det_modpath_extensions","title":"Determine module path extensions, if any. Examples: Compiler/GCC/4.8.3 (for GCC/4.8.3 module), MPI/GCC/4.8.3/OpenMPI/1.6.5 (for OpenMPI/1.6.5 module)
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/hierarchical_mns/#easybuild.tools.module_naming_scheme.hierarchical_mns.HierarchicalMNS.det_module_subdir","title":"Determine module subdirectory, relative to the top of the module path. This determines the separation between module names exposed to users, and what's part of the $MODULEPATH. Examples: Core, Compiler/GCC/4.8.3, MPI/GCC/4.8.3/OpenMPI/1.6.5
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/hierarchical_mns/#easybuild.tools.module_naming_scheme.hierarchical_mns.HierarchicalMNS.det_module_symlink_paths","title":"Determine list of paths in which symlinks to module files must be created.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/hierarchical_mns/#easybuild.tools.module_naming_scheme.hierarchical_mns.HierarchicalMNS.det_short_module_name","title":"Determine short module name, i.e. the name under which modules will be exposed to users. Examples: GCC/4.8.3, OpenMPI/1.6.5, OpenBLAS/0.2.9, HPL/2.1, Python/2.7.5
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/hierarchical_mns/#easybuild.tools.module_naming_scheme.hierarchical_mns.HierarchicalMNS.det_toolchain_compilers_name_version","title":"Determine toolchain compiler tag, for given list of compilers.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/hierarchical_mns/#easybuild.tools.module_naming_scheme.hierarchical_mns.HierarchicalMNS.expand_toolchain_load","title":"Determine whether load statements for a toolchain should be expanded to load statements for its dependencies. This is useful when toolchains are not exposed to users.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/hierarchical_mns/#easybuild.tools.module_naming_scheme.hierarchical_mns.HierarchicalMNS.requires_toolchain_details","title":"Determine whether toolchain details are required by this module naming scheme, e.g. whether one of det_toolchain_* functions are relied upon.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns/","title":"migrate_from_eb_to_hmns","text":"Implementation of a module naming scheme that can be used to migrate from EasyBuildMNS to HierarchicalMNS.
Determine name of software installation subdirectory of install path, using EasyBuild MNS.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/","title":"mns","text":"Module naming scheme API.
Abstract class for a module naming scheme implementation.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/#easybuild.tools.module_naming_scheme.mns.ModuleNamingScheme.__init__","title":"Initialize logger.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/#easybuild.tools.module_naming_scheme.mns.ModuleNamingScheme.det_full_module_name","title":"Determine full module name, relative to the top of the module path.
PARAMETER DESCRIPTION dict-like object with easyconfig parameter values; for now only the 'name', 'version', 'versionsuffix' and 'toolchain' parameters are guaranteed to be available
string with full module name, e.g.: '///'","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/#easybuild.tools.module_naming_scheme.mns.ModuleNamingScheme.det_init_modulepaths","title":"det_init_modulepaths(ec)","text":"
Determine initial module paths, where the modules that are top of the hierarchy (if any) live.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/#easybuild.tools.module_naming_scheme.mns.ModuleNamingScheme.det_install_subdir","title":"Determine name of software installation subdirectory of install path.
PARAMETER DESCRIPTION dict-like object with easyconfig parameter values; for now only the 'name', 'version', 'versionsuffix' and 'toolchain' parameters are guaranteed to be available
string with name of subdirectory, e.g.: '///'","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/#easybuild.tools.module_naming_scheme.mns.ModuleNamingScheme.det_make_devel_module","title":"det_make_devel_module()","text":"
Determine if a devel module should be generated. Can be used to create a separate set of modules with a different naming scheme. Software is already installed beforehand with one naming scheme, including development module.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/#easybuild.tools.module_naming_scheme.mns.ModuleNamingScheme.det_modpath_extensions","title":"Determine list of subdirectories for which to extend $MODULEPATH with when this module is loaded (if any).
PARAMETER DESCRIPTION dict-like object with easyconfig parameter values; for now only the 'name', 'version', 'versionsuffix' and 'toolchain' parameters are guaranteed to be available
A list of $MODULEPATH subdirectories.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/#easybuild.tools.module_naming_scheme.mns.ModuleNamingScheme.det_module_subdir","title":"Determine subdirectory for module file in $MODULEPATH. This determines the separation between module names exposed to users, and what's part of the $MODULEPATH.
PARAMETER DESCRIPTION dict-like object with easyconfig parameter values; for now only the 'name', 'version', 'versionsuffix' and 'toolchain' parameters are guaranteed to be available
string with subdir path (relative to $MODULEPATH), e.g. '/'","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/#easybuild.tools.module_naming_scheme.mns.ModuleNamingScheme.det_module_symlink_paths","title":"det_module_symlink_paths(ec)","text":"
Determine list of paths in which symlinks to module files must be created.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/#easybuild.tools.module_naming_scheme.mns.ModuleNamingScheme.det_short_module_name","title":"Determine short module name, i.e. the name under which modules will be exposed to users.
PARAMETER DESCRIPTION dict-like object with easyconfig parameter values; for now only the 'name', 'version', 'versionsuffix' and 'toolchain' parameters are guaranteed to be available
string with module name, e.g. '/'","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/#easybuild.tools.module_naming_scheme.mns.ModuleNamingScheme.det_user_modpath_extensions","title":"det_user_modpath_extensions(ec)","text":"
Determine list of subdirectories relative to the user-specific modules directory for which to extend $MODULEPATH with when this module is loaded (if any).
PARAMETER DESCRIPTION dict-like object with easyconfig parameter values; for now only the 'name', 'version', 'versionsuffix' and 'toolchain' parameters are guaranteed to be available
A list of $MODULEPATH subdirectories.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/#easybuild.tools.module_naming_scheme.mns.ModuleNamingScheme.expand_toolchain_load","title":"Determine whether load statements for a toolchain should be expanded to load statements for its dependencies. This is useful when toolchains are not exposed to users.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/#easybuild.tools.module_naming_scheme.mns.ModuleNamingScheme.is_short_modname_for","title":"Determine whether the specified (short) module name is a module for software with the specified name. Default implementation checks via a strict regex pattern, and assumes short module names are of the form: /[-]","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/#easybuild.tools.module_naming_scheme.mns.ModuleNamingScheme.is_sufficient","title":"is_sufficient(keys)","text":"
Determine whether specified list of easyconfig parameters is sufficient for this module naming scheme.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/mns/#easybuild.tools.module_naming_scheme.mns.ModuleNamingScheme.requires_toolchain_details","title":"Determine whether toolchain details are required by this module naming scheme, e.g. whether one of det_toolchain_* functions are relied upon.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/toolchain/","title":"toolchain","text":"Toolchain querying support for module naming schemes.
Determine compilers of toolchain for given EasyConfig instance.
PARAMETER DESCRIPTION a parsed EasyConfig file (an AttributeError will occur if a simple dict is passed)
Determine details of a particular toolchain element, for a given Toolchain instance.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/toolchain/#easybuild.tools.module_naming_scheme.toolchain.det_toolchain_mpi","title":"Determine MPI library of toolchain for given EasyConfig instance.
PARAMETER DESCRIPTION a parsed EasyConfig file (an AttributeError will occur if a simple dict is passed)
Utility functions for implementating module naming schemes.
Returns a list of available module naming schemes.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/utilities/#easybuild.tools.module_naming_scheme.utilities.det_full_ec_version","title":"Determine exact install version, based on supplied easyconfig. e.g. 1.2.3-goalf-1.1.0-no-OFED or 1.2.3 (for system toolchains)
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/utilities/#easybuild.tools.module_naming_scheme.utilities.det_hidden_modname","title":"Determine the hidden equivalent of the specified module name.
","boost":0.5},{"location":"api/easybuild/tools/module_naming_scheme/utilities/#easybuild.tools.module_naming_scheme.utilities.is_valid_module_name","title":"Check whether the specified value is a valid module name.
","boost":0.5},{"location":"api/easybuild/tools/package/","title":"package","text":"Various utilities related to packaging support.
The wrapper class for Package Naming Schemes.
","boost":0.5},{"location":"api/easybuild/tools/package/utilities/#easybuild.tools.package.utilities.ActivePNS.__init__","title":"Returns the list of valed naming schemes They are loaded from the easybuild.package.package_naming_scheme namespace
","boost":0.5},{"location":"api/easybuild/tools/package/utilities/#easybuild.tools.package.utilities.check_pkg_support","title":"Check whether packaging is possible, if required dependencies are available.
","boost":0.5},{"location":"api/easybuild/tools/package/utilities/#easybuild.tools.package.utilities.package","title":"Package installed software, according to active packaging configuration settings.
","boost":0.5},{"location":"api/easybuild/tools/package/utilities/#easybuild.tools.package.utilities.package_with_fpm","title":"This function will build a package using fpm and return the directory where the packages are
","boost":0.5},{"location":"api/easybuild/tools/package/package_naming_scheme/","title":"package_naming_scheme","text":":author: Robert Schmidt (Ottawa Hospital Research Institute) :author: Kenneth Hoste (Ghent University) :author: Martin Budsj\u00f6 (VolvoCars)
","boost":0.5},{"location":"api/easybuild/tools/package/package_naming_scheme/easybuild_deb_friendly_pns/#easybuild.tools.package.package_naming_scheme.easybuild_deb_friendly_pns.EasyBuildDebFriendlyPNS","title":"Class implmenting the Deb friendly EasyBuild packaging naming scheme.
","boost":0.5},{"location":"api/easybuild/tools/package/package_naming_scheme/easybuild_deb_friendly_pns/#easybuild.tools.package.package_naming_scheme.easybuild_deb_friendly_pns.EasyBuildDebFriendlyPNS.version","title":"Determine package version: EasyBuild version used to build & install.
","boost":0.5},{"location":"api/easybuild/tools/package/package_naming_scheme/easybuild_pns/","title":"easybuild_pns","text":"Class implmenting the default EasyBuild packaging naming scheme.
","boost":0.5},{"location":"api/easybuild/tools/package/package_naming_scheme/easybuild_pns/#easybuild.tools.package.package_naming_scheme.easybuild_pns.EasyBuildPNS.name","title":"Determine package version: EasyBuild version used to build & install.
","boost":0.5},{"location":"api/easybuild/tools/package/package_naming_scheme/pns/","title":"pns","text":"Abstract implementation of a package naming scheme.
initialize logger.
","boost":0.5},{"location":"api/easybuild/tools/package/package_naming_scheme/pns/#easybuild.tools.package.package_naming_scheme.pns.PackageNamingScheme.name","title":"Determine package version.
","boost":0.5},{"location":"api/easybuild/tools/py2vs3/","title":"py2vs3","text":"Functionality to facilitate keeping code compatible with Python 2 & Python 3.
Implementations for Python 3.
Extract method name from lambda function.
","boost":0.5},{"location":"api/easybuild/tools/py2vs3/py2/#easybuild.tools.py2vs3.py2.json_loads","title":"Wrapper for json.loads that takes into account that Python versions older than 3.6 require a string value.
","boost":0.5},{"location":"api/easybuild/tools/py2vs3/py2/#easybuild.tools.py2vs3.py2.load_source","title":"Raise exception of specified class with given message and traceback.
","boost":0.5},{"location":"api/easybuild/tools/py2vs3/py2/#easybuild.tools.py2vs3.py2.safe_cmp_looseversions","title":"Safe comparison function for two (values containing) LooseVersion instances.
","boost":0.5},{"location":"api/easybuild/tools/py2vs3/py2/#easybuild.tools.py2vs3.py2.sort_looseversions","title":"Sort list of (values including) distutils.version.LooseVersion instances.
","boost":0.5},{"location":"api/easybuild/tools/py2vs3/py2/#easybuild.tools.py2vs3.py2.subprocess_popen_text","title":"Call subprocess.Popen in text mode with specified named arguments.
","boost":0.5},{"location":"api/easybuild/tools/py2vs3/py2/#easybuild.tools.py2vs3.py2.subprocess_terminate","title":"Functionality to facilitate keeping code compatible with Python 2 & Python 3.
Implementations for Python 3.
Extract method name from lambda function.
","boost":0.5},{"location":"api/easybuild/tools/py2vs3/py3/#easybuild.tools.py2vs3.py3.json_loads","title":"Wrapper for json.loads that takes into account that Python versions older than 3.6 require a string value.
","boost":0.5},{"location":"api/easybuild/tools/py2vs3/py3/#easybuild.tools.py2vs3.py3.load_source","title":"Raise exception of specified class with given message and traceback.
","boost":0.5},{"location":"api/easybuild/tools/py2vs3/py3/#easybuild.tools.py2vs3.py3.safe_cmp_looseversions","title":"Safe comparison function for two (values containing) LooseVersion instances.
","boost":0.5},{"location":"api/easybuild/tools/py2vs3/py3/#easybuild.tools.py2vs3.py3.sort_looseversions","title":"Sort list of (values including) distutils.version.LooseVersion instances.
","boost":0.5},{"location":"api/easybuild/tools/py2vs3/py3/#easybuild.tools.py2vs3.py3.subprocess_popen_text","title":"Call subprocess.Popen in text mode with specified named arguments.
","boost":0.5},{"location":"api/easybuild/tools/py2vs3/py3/#easybuild.tools.py2vs3.py3.subprocess_terminate","title":"Class for file repositories.
","boost":0.5},{"location":"api/easybuild/tools/repository/filerepo/#easybuild.tools.repository.filerepo.FileRepository.add_easyconfig","title":"software install version, incl. toolchain & versionsuffix
for file based repos this will create the repo directory if it doesn't exist.
Class for git repositories.
","boost":0.5},{"location":"api/easybuild/tools/repository/gitrepo/#easybuild.tools.repository.gitrepo.GitRepository.__init__","title":"Initialize git client to None (will be set later) All the real logic is in the setup_repo and create_working_copy methods
","boost":0.5},{"location":"api/easybuild/tools/repository/gitrepo/#easybuild.tools.repository.gitrepo.GitRepository.add_easyconfig","title":"software install version, incl. toolchain & versionsuffix
Clean up git working copy.
","boost":0.5},{"location":"api/easybuild/tools/repository/gitrepo/#easybuild.tools.repository.gitrepo.GitRepository.commit","title":"Create git working copy.
","boost":0.5},{"location":"api/easybuild/tools/repository/gitrepo/#easybuild.tools.repository.gitrepo.GitRepository.setup_repo","title":"Set up git repository.
","boost":0.5},{"location":"api/easybuild/tools/repository/gitrepo/#easybuild.tools.repository.gitrepo.GitRepository.stage_file","title":"Class for hg repositories.
","boost":0.5},{"location":"api/easybuild/tools/repository/hgrepo/#easybuild.tools.repository.hgrepo.HgRepository.__init__","title":"Initialize mercurial client to None (will be set later) All the real logic is in the setup_repo and create_working_copy methods
","boost":0.5},{"location":"api/easybuild/tools/repository/hgrepo/#easybuild.tools.repository.hgrepo.HgRepository.add_easyconfig","title":"software install version, incl. toolchain & versionsuffix
Clean up mercurial working copy.
","boost":0.5},{"location":"api/easybuild/tools/repository/hgrepo/#easybuild.tools.repository.hgrepo.HgRepository.commit","title":"Create mercurial working copy.
","boost":0.5},{"location":"api/easybuild/tools/repository/hgrepo/#easybuild.tools.repository.hgrepo.HgRepository.setup_repo","title":"Set up mercurial repository.
","boost":0.5},{"location":"api/easybuild/tools/repository/hgrepo/#easybuild.tools.repository.hgrepo.HgRepository.stage_file","title":"Initialize a repository. self.repo and self.subdir will be set. self.wc will be set to None. Then, setup_repo and create_working_copy will be called (in that order)
","boost":0.5},{"location":"api/easybuild/tools/repository/repository/#easybuild.tools.repository.repository.Repository.add_easyconfig","title":"software install version, incl. toolchain & versionsuffix
Clean up working copy.
","boost":0.5},{"location":"api/easybuild/tools/repository/repository/#easybuild.tools.repository.repository.Repository.commit","title":"Create working copy.
","boost":0.5},{"location":"api/easybuild/tools/repository/repository/#easybuild.tools.repository.repository.Repository.get_buildstats","title":"Prepare repository for use.
","boost":0.5},{"location":"api/easybuild/tools/repository/repository/#easybuild.tools.repository.repository.Repository.is_initialized","title":"Indicate whether repository was initialized.
","boost":0.5},{"location":"api/easybuild/tools/repository/repository/#easybuild.tools.repository.repository.Repository.setup_repo","title":"Set up repository.
","boost":0.5},{"location":"api/easybuild/tools/repository/repository/#easybuild.tools.repository.repository.Repository.stage_file","title":"Return all available repositories. check_useable: boolean, if True, only return usable repositories
","boost":0.5},{"location":"api/easybuild/tools/repository/repository/#easybuild.tools.repository.repository.init_repository","title":"Return an instance of the selected repository class.
","boost":0.5},{"location":"api/easybuild/tools/repository/svnrepo/","title":"svnrepo","text":"Set self.client to None. Real logic is in setup_repo and create_working_copy
","boost":0.5},{"location":"api/easybuild/tools/repository/svnrepo/#easybuild.tools.repository.svnrepo.SvnRepository.add_easyconfig","title":"software install version, incl. toolchain & versionsuffix
Clean up SVN working copy.
","boost":0.5},{"location":"api/easybuild/tools/repository/svnrepo/#easybuild.tools.repository.svnrepo.SvnRepository.commit","title":"Create SVN working copy.
","boost":0.5},{"location":"api/easybuild/tools/repository/svnrepo/#easybuild.tools.repository.svnrepo.SvnRepository.setup_repo","title":"Set up SVN repository.
","boost":0.5},{"location":"api/easybuild/tools/repository/svnrepo/#easybuild.tools.repository.svnrepo.SvnRepository.stage_file","title":"Toolchain compiler module, provides abstract class for compilers.
General compiler-like class can't be used without creating new class C(Compiler,Toolchain)
","boost":0.5},{"location":"api/easybuild/tools/toolchain/compiler/#easybuild.tools.toolchain.compiler.Compiler.__init__","title":"Compiler constructor.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/compiler/#easybuild.tools.toolchain.compiler.Compiler.comp_family","title":"Return compiler family used in this toolchain. @prefix: Prefix for compiler (e.g. 'CUDA_').
","boost":0.5},{"location":"api/easybuild/tools/toolchain/compiler/#easybuild.tools.toolchain.compiler.Compiler.set_options","title":"Process compiler toolchain options.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/compiler/#easybuild.tools.toolchain.compiler.Compiler.set_variables","title":"Create an infix based on the given prefix.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/constants/","title":"constants","text":"Toolchain fft module, provides abstract class for FFT libraries.
Toolchain linalg module. Contains all (scalable) linear algebra related classes
General LinearAlgebra-like class can't be used without creating new class S(LinAlg) To provide the BLAS/LAPACK/ScaLAPACK tools
","boost":0.5},{"location":"api/easybuild/tools/toolchain/linalg/#easybuild.tools.toolchain.linalg.LinAlg.blas_family","title":"Return type of BLAS library used in this toolchain.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/linalg/#easybuild.tools.toolchain.linalg.LinAlg.lapack_family","title":"Return type of LAPACK library used in this toolchain.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/linalg/#easybuild.tools.toolchain.linalg.LinAlg.set_variables","title":"Toolchain mpi module. Contains all MPI related classes
Construct an MPI command for the given command and number of ranks.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/mpi/#easybuild.tools.toolchain.mpi.Mpi.mpi_cmd_prefix","title":"Return type of MPI library used in this toolchain.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/mpi/#easybuild.tools.toolchain.mpi.Mpi.set_variables","title":"Return template for MPI command, for specified MPI family.
PARAMETER DESCRIPTION The toolchain options module contains the ToolchainOptions class These are the options that can be passed to the toolchain through the easyconfig files
Map values can be string with named templates By default following named options is filled %(opt)s : option name %(value)s : option value
Add @options: dict with options : tuple option_name and option_description @options_map: dict with a mapping between and option and a value
","boost":0.5},{"location":"api/easybuild/tools/toolchain/options/#easybuild.tools.toolchain.options.ToolchainOptions.option","title":"The toolchain module with the abstract Toolchain class.
Creating a new toolchain should be as simple as possible.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain--toolchain-terminology","title":"Toolchain terminology","text":"Toolchain: group of development related utilities (eg compiler) and libraries (eg MPI, linear algebra) -> eg tc=Toolchain()
Toolchain options : options passed to the toolchain through the easyconfig file -> eg tc.options
Options : all options passed to an executable Flags: specific subset of options, typically involved with compilation -> eg tc.variables.CFLAGS LinkOptions: specific subset of options, typically involved with linking -> eg tc.variables.LIBBLAS
TooclchainVariables: list of environment variables that are set when the toolchain is initialised and the toolchain options have been parsed. -> eg tc.variables['X'] will be available as os.environ['X']
Toolchain constructor.
PARAMETER DESCRIPTION [DEPRECATED] Verify if the given dependencies exist, and return them.
This method is deprecated. You should pass the dependencies to the 'prepare' method instead, via the 'deps' named argument.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.as_dict","title":"Return toolchain specification as a dictionary.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.banned_linked_shared_libs","title":"List of shared libraries (names, file names, paths) which are not allowed to be linked in any installed binary/library.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.base_init","title":"Initialise missing class attributes (log, options, variables).
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.blas_family","title":"Return type of BLAS library used in this toolchain, or 'None' if BLAS is not supported.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.cleanup","title":"Determine list of relevant compilers for specified compiler caching tool.
PARAMETER DESCRIPTION Return compiler family used in this toolchain (abstract method).
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.compilers","title":"Determine toolchain elements for given Toolchain instance.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.det_short_module_name","title":"Determine module name for this toolchain.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.generate_vars","title":"Get compiler flag(s) for a certain option.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.get_software_root","title":"Get value for specified variable. typ: indicates what type of return value is expected
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.handle_sysroot","title":"Extra stuff to be done when alternate system root is specified via --sysroot EasyBuild configuration option.
Check whether a specific software name is listed as a dependency in the module for this toolchain.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.is_deprecated","title":"Return whether or not this toolchain is deprecated.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.is_required","title":"Determine whether this is a required toolchain element.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.is_rpath_wrapper","title":"Check whether command at specified location already is an RPATH wrapper script rather than the actual command
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.is_system_toolchain","title":"Return boolean to indicate whether this toolchain is a system(/dummy) toolchain.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.lapack_family","title":"Return type of LAPACK library used in this toolchain, or 'None' if LAPACK is not supported.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.mpi_family","title":"Return type of MPI library used in this toolchain, or 'None' if MPI is not supported.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.prepare","title":"Prepare a set of environment parameters based on name/version of toolchain - load modules for toolchain and dependencies - generate extra variables and set them in the environment
PARAMETER DESCRIPTION boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (If string: comma separated list of variables that will be ignored).
whether or not to (re)load the toolchain module, and the modules for the dependencies
extra directories to include in RPATH filter (e.g. build dir, tmpdir, ...)
extra directories to include in RPATH filter (e.g. build dir, tmpdir, ...)
List of shared libraries (names, file names, paths) which must be linked in all installed binaries/libraries.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.reset","title":"Reset this toolchain instance.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.set_minimal_build_env","title":"Set up a minimal build environment, by setting (only) the $CC and $CXX environment variables.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.set_options","title":"Do nothing? Everything should have been set by others Needs to be defined for super() relations
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.show_variables","title":"Create a symlink for each command to binary/script at specified path.
PARAMETER DESCRIPTION Return toolchain family for this toolchain.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.Toolchain.variables_init","title":"Initialise toolchain variables.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.env_vars_external_module","title":"Determine $EBROOT and/or $EBVERSION environment variables that can be set for external module, based on the provided name, version and metadata.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchain/#easybuild.tools.toolchain.toolchain.is_system_toolchain","title":"Return whether toolchain with specified name is a system toolchain or not.
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchainvariables/","title":"toolchainvariables","text":"Class to hold variable-like key/value pairs in context of compilers (i.e. the generated string are e.g. compiler options or link flags)
","boost":0.5},{"location":"api/easybuild/tools/toolchain/toolchainvariables/#easybuild.tools.toolchain.toolchainvariables.ToolchainVariables.add_begin_end_linkerflags","title":"For given lib if toggle_startstopgroup: toggle begin/end group if toggle_staticdynamic: toggle static/dynamic
","boost":0.5},{"location":"api/easybuild/tools/toolchain/utilities/","title":"utilities","text":"Return an initialized toolchain for the given specifications. If none is available in the toolchain instances cache, a new one is created.
PARAMETER DESCRIPTION toolchain dependencies (i.e. toolchain components)
Obtain a Toolchain instance for the toolchain with specified name, next to a list of available toolchains.
PARAMETER DESCRIPTION Command and flags list First of the list has no prefix (i.e. the executable) The remainder of the options are considered flags
","boost":0.5},{"location":"api/easybuild/tools/toolchain/variables/#easybuild.tools.toolchain.variables.FlagList","title":"This page provides a concise overview of the most prominent changes in EasyBuild version 4.0, compared to the latest EasyBuild v3.x (version 3.9.4).
A detailed overview with links to the pull requests in which the changes are made is available in the EasyBuild release notes (see EasyBuild v4.0.0 (September 20th 2019) in particular).
"},{"location":"easybuild-v4/overview-of-changes/#eb4_changes_significant_enhancements","title":"Significant enhancements in EasyBuild v4.0","text":"To simplify the installation of EasyBuild, no Python packages other than the ones included in the Python standard library are required for EasyBuild v4.0. More specifically:
Note that specific Python packages may currently still be required for certain EasyBuild functionality outside of the core functionality of building and installing scientific software, including keyring for the GitHub integration features (see Integration with GitHub), etc.
"},{"location":"easybuild-v4/overview-of-changes/#eb4_python3_support","title":"Support for running EasyBuild on top of Python 3","text":"A significant effort has been made to ensure that the EasyBuild framework and the easyblocks included with EasyBuild are compatible with Python 3, while retaining the compatibility with Python 2.
A couple of additional custom software-specific easyblocks were added in EasyBuild v4.0, including:
In addition, various (generic and software-specific) easyblocks were improved and enhanced (see EasyBuild release notes for more details).
"},{"location":"easybuild-v4/overview-of-changes/#eb4_2019b_common_toolchains","title":"2019b update of common toolchains","text":"A recommended naming scheme for local variables in easyconfig files was introduced.
If an easyconfig file contains local variables that do not follow the recommended naming scheme, a warning will be printed (by default).
For more information, see Local variables in easyconfig files.
"},{"location":"easybuild-v4/overview-of-changes/#eb4_changes_backwards_incompatible","title":"Backwards-incompatible changes in EasyBuild v4.0","text":"Other than the changed default configuration, these changes are mainly important for developers of the EasyBuild framework and easyblock implementers.
"},{"location":"easybuild-v4/overview-of-changes/#eb4_changes_fixed_installdir_naming_scheme","title":"With this configuration setting enabled, the name of software installation directories will match the module name generated by the (default) EasyBuildMNS module naming scheme.
This change was done to make it easier to generate module files using one or more additional module naming scheme (using --module-only) for already existing software installations. Only when the name of the software installation directories is independent of the module naming scheme being used during the (first) installation is it possible to later generate additional module files using a different module naming scheme.
Mixing different naming schemes for software installations directories in a single software stack works just fine; it's mostly a matter of inconsistency that could be confusing for humans.
"},{"location":"easybuild-v4/overview-of-changes/#eb4_changes_fixed_installdir_naming_scheme_disabling","title":"Disabling A limited number of functions, classes and constants have been relocated in the EasyBuild framework.
Making EasyBuild compatible with Python 3 also required some similar changes, see Functions & classes that must be imported from the easybuild.tools.py2vs3 namespace.
A detailed overview of relocated functions and constants is available at Overview of relocated functions, classes and constants in EasyBuild v4.0.
"},{"location":"easybuild-v4/overview-of-changes/#eb4_changes_ingested_vsc_base","title":"Ingested functionality from A number of specific functions and classes have been placed in existing modules in the easybuild.tools package instead.
The affected functions are listed in Overview of relocated functions, classes and constants in EasyBuild v4.0.
"},{"location":"easybuild-v4/overview-of-changes/#eb4_changes_ingested_vsc_base_fake_vsc_namespace","title":"Fake A handful functions and classes that could be imported directly from the Python standard library should now be imported from the easybuild.tools.py2vs3 namespace instead (perhaps under a different name), to ensure compatibility with Python 2 and 3.
See Compatibility with Python 2 and Python 3 for more information.
The affected functions are also included in Overview of relocated functions, classes and constants in EasyBuild v4.0.
"},{"location":"easybuild-v4/overview-of-changes/#eb4_changes_deprecated","title":"Deprecated functionality in EasyBuild v4.0","text":"Some functionality was deprecated in EasyBuild v4.0, and will no longer be supported in EasyBuild v5.0.
If you trigger any deprecated functionality, a warning message will be printed.
"},{"location":"easybuild-v4/overview-of-changes/#eb4_changes_dummy_tc","title":"Deprecated For more information, please consult System toolchain.
"},{"location":"easybuild-v4/overview-relocated-functions-constants/","title":"Overview of relocated functions, classes and constants in EasyBuild v4.0","text":"This page provides an alphabetical overview of relocated functions, classes and constants in EasyBuild version 4.0; see Backwards-incompatible changes in EasyBuild v4.0 for motivation and high-level information.
"},{"location":"easybuild-v4/overview-relocated-functions-constants/#eb4_relocated_basestring","title":"See also Compatibility with Python 2 and Python 3.
"},{"location":"easybuild-v4/overview-relocated-functions-constants/#eb4_relocated_configparser","title":"See also Compatibility with Python 2 and Python 3.
"},{"location":"easybuild-v4/overview-relocated-functions-constants/#eb4_relocated_DEVEL_MODULE_SUFFIX","title":"See also Compatibility with Python 2 and Python 3.
"},{"location":"easybuild-v4/overview-relocated-functions-constants/#eb4_relocated_reload","title":"See also Compatibility with Python 2 and Python 3.
"},{"location":"easybuild-v4/overview-relocated-functions-constants/#eb4_relocated_shell_quote","title":"See also Compatibility with Python 2 and Python 3.
"},{"location":"easybuild-v4/overview-relocated-functions-constants/#eb4_relocated_subprocess_Popen","title":"See also Compatibility with Python 2 and Python 3.
"},{"location":"easybuild-v4/overview-relocated-functions-constants/#eb4_relocated_urlencode","title":"See also Compatibility with Python 2 and Python 3.
"},{"location":"easybuild-v4/overview-relocated-functions-constants/#eb4_relocated_urllib","title":"See also Compatibility with Python 2 and Python 3.
"},{"location":"easybuild-v4/overview-relocated-functions-constants/#eb4_relocated_urllib2","title":"See also Compatibility with Python 2 and Python 3.
"},{"location":"easybuild-v4/overview-relocated-functions-constants/#eb4_relocated_vsc_utils_modules","title":"See also No more required Python packages.
"},{"location":"easybuild-v5/","title":"EasyBuild v5.0","text":"EasyBuild 5.0 requires Python >= 3.6 to run.
Running EasyBuild with Python 2.7 or a Python 3 version older than Python 3.6 is no longer supported.
Trying to run EasyBuild with a Python version that is too old will result in an error:
Python 2.7 has been end-of-life since 1 Jan 2020, and dropping compatibility with Python 2.7 and Python 3.5 enabled some significant code cleanup (see easybuild-framework PR #4229).
The results of the 6th EasyBuild User Survey (2022) show that the impact of this breaking change on the EasyBuild community should be very limited, since:
Along with actively removing code that was only required to retain compatibility with Python 2.7 or 3.5, the easybuild.tools.py2vs3 module that was introduced to facilitate supporting both Python 2.7 and Python 3 has been deprecated (see also here).
"},{"location":"easybuild-v5/backwards-incompatible-changes/#bootstrap_script","title":"Deprecated EasyBuild bootstrap script is removed","text":"The EasyBuild bootstrap script has been removed (see easybuild-framework PR #4233).
Please see the installation page for the suggested methods for installing EasyBuild.
"},{"location":"easybuild-v5/backwards-incompatible-changes/#yeb","title":"Experimental support for the .yeb easyconfig format is removed","text":"This format allowed easyconfigs to be specified in YAML. However, there has been no recent development of this format and little suggestion that anyone was using it at all.
"},{"location":"easybuild-v5/changes-in-default-configuration/","title":"Changes in default configuration in EasyBuild v5.0","text":"RPATH linking is enabled by default in EasyBuild v5.0 (see easybuild-framework PR #4448).
The benefits for enabling RPATH are explained in Why RPATH?.
This enhancement does not add any filtering of environment variables. This means $LD_LIBRARY_PATH will continue to be appended by the environment module files EasyBuild generates, unless it is configured to filter these variables (via --filter-env-vars, see also Relation to $LD_LIBRARY_PATH).
Some functionality is being deprecated in EasyBuild v5.0, and will no longer be supported in EasyBuild v6.0:
If you trigger any deprecated functionality when using EasyBuild v5.0, a warning message will be printed.
"},{"location":"easybuild-v5/deprecated-functionality/#run_cmd","title":"EasyBuild v5 now uses a range of ~50 exit codes instead of just 0 for normal termination and 1 for unexpected termination. Each non-zero exit code correlates to the specific type of error or failure that caused the termination of the program. For instance, a missing easyconfig or a failed checksum check. The full list of exit codes is defined in the class easybuild.tools.build_log.EasyBuildExit.
EasyBuild will always return its own exit codes on termination. Other exit codes from external processes executed through run_shell_cmd or HTTP response status codes are reported in the corresponding logs.
"},{"location":"easybuild-v5/enhancements/#reproducible_tarballs","title":"Reproducible tarballs","text":"EasyBuild can now generate reproducible tarballs of sources cloned from Git repositories. This means that those sources using the git_config option will now have consistent contents across different systems and across time, allowing to reliably validate them with checksums. EasyBuild follows the archival guidelines from reproducible-builds.org to generate those reproducible tarballs.
We intend to update this section of the documentation regularly as the planned changes are being implemented.
This page provides a concise overview of the most prominent changes in EasyBuild version 5.0, which can be categorized as:
For in-depth details on a particular change, see the pull requests that are linked from each of the subsections linked above.
At the EasyBuild User Meeting 2023, Simon Branford set out the roadmap for EasyBuild v5.0.
To track the progress on the development of EasyBuild v5.0, see the GitHub Project board for EasyBuild v5.0.
This section covers the major planned changes.
It is not intended to be a complete list of all changes that are planned for EasyBuild v5.0.
"},{"location":"easybuild-v5/policies/","title":"Policies related to EasyBuild v5.0","text":"Starting with EasyBuild v5.0, we will enforce the new toolchain support policy.
"},{"location":"easybuild-v5/run_shell_cmd/","title":"For parameters in general, the following translation table can be used, where the default values are shown:
run_cmd / run_cmd_qa parameter run_shell_cmd parameter meaning If you are a new user of EasyBuild you can safely ignore everything below this line, refer instead to Configuring EasyBuild.
"},{"location":"legacy/configuration/#porting-from-legacy-configuration-style","title":"Porting from legacy configuration style","text":"In EasyBuild v1.x, a couple of configuration options, other than the standard ones aligned with variables, are available that follow the legacy configuration style, including:
Likewise, the following legacy environment variables allowed to override selected configuration settings:
We strongly advise to switch to the new way of configuring EasyBuild as soon as possible, since the legacy configuration style will no longer be supported in EasyBuild v2.x.
"},{"location":"legacy/configuration/#how-easybuild-used-to-be-configured-in-the-early-days","title":"How EasyBuild used to be configured in the early days","text":"Configuring EasyBuild is done by providing a configuration file.
EasyBuild expects the configuration file to contain valid Python code, because it executes its contents (using exec). The rationale is that this approach provides a lot of flexibility for configuring EasyBuild.
EasyBuild will use the file that is provided by the path/filename in the following order of preference:
Note that the build directories are emptied by EasyBuild when the installation is completed (by default).
"},{"location":"legacy/configuration/#install-path-required","title":"Install path (required)","text":"It is probably a good idea to add this to your (favourite) shell .rc file, e.g., .bashrc, and/or the .profile login scripts, so you do not need to adjust the $MODULEPATH variable every time you start a new session.
"},{"location":"legacy/configuration/#source-path-required","title":"Source path (required)","text":"Similarly to the configuration file lookup, EasyBuild looks for the installation files as given by the sources variable in the .eb easyconfig file, in the following order of preference:
Note that these locations are also used when EasyBuild looks for patch files in addition to the various easybuild/easyconfigs directories that are listed in the $PYTHONPATH.
"},{"location":"policies/toolchains/","title":"Supported Toolchain Generations Policy","text":"For the central EasyBuild repositories, we support a set of toolchain generations.
The central easyconfigs repository is intended to provide references easyconfigs. For the reference easyconfigs we aim to have only one version of a software being used as a dependency in each toolchain generation. (There are exceptions, but we aim to keep these limited.)
Sites and users can then supplement these easyconfigs via there own collection of easyconfigs. This additional collection is added via the robot search path.
"},{"location":"policies/toolchains/#current-situation","title":"Current situation","text":"Changes coming in EasyBuild 5.0 relevant to EasyBuild contributors.
Changes coming in EasyBuild 5.0 relevant to EasyBuild developers.
...
"},{"location":"roles/end-users/","title":"For end users","text":""},{"location":"roles/end-users/#easybuild-50","title":"EasyBuild 5.0","text":"Changes coming in EasyBuild 5.0 relevant to EasyBuild users.
...
Changes coming in EasyBuild 5.0 relevant to EasyBuild maintainers.
Changes coming in EasyBuild 5.0 relevant to user support teams.
This page currently presents the raw results of the 6th EasyBuild User Survey, which was held in March 2023.
Additional text will be added to help interpret the results soon.
The results of the EasyBuild User Survey are assumed to give a fairly representative view on the EasyBuild community, but they should be interpreted with a grain of salt, since there is no doubt significant bias in terms of participants.
Participation in the EasyBuild User Survey has been growing steadily over the years, to 118 participants in the 6th survey which was held March 2023.
For the previous survey, the majority of the participants were made aware of it via the EasyBuild mailing list (~42%) and the EasyBuild Slack (~34%).
While these two channels were still the most prominent for this survey, it is now the EasyBuild Slack that is the largest trigger to participate in the survey: ~47% (vs 27% via the EasyBuild mailing list).
"},{"location":"user-survey/#demographics","title":"Demographics","text":""},{"location":"user-survey/#easybuild-adoption-and-experience","title":"EasyBuild: adoption and experience","text":""},{"location":"user-survey/#operating-system","title":"Operating system","text":""},{"location":"user-survey/#python-version","title":"Python version","text":""},{"location":"user-survey/#system-aspects","title":"System aspects","text":""},{"location":"user-survey/#cpus","title":"CPUs","text":""},{"location":"user-survey/#gpus","title":"GPUs","text":""},{"location":"user-survey/#top500","title":"Top500","text":"Significant increase in use of NVHPC-based toolchains (21%, was 15% and 7% in previous surveys).
This page will soon replace https://docs.easybuild.io/en/latest/eb_a_e_EB_WRF.html.
** It still needs to be ported from reStructuredText (.rst) to MarkDown (.md), and you can help with that! **
See https://github.com/easybuilders/easybuild-docs for more information.
"},{"location":"version-specific/eb-help/","title":"EasyBuild configuration options","text":"Builds software based on easyconfig (or parse a directory). Provide one or more easyconfigs or directories, use -H or --help more information.
"},{"location":"version-specific/eb-help/#help-options","title":"Help options","text":"Option flag Option description BinariesTarball - Binary - BuildEnv - Bundle - CMakeMake - CMakeMakeCp - CMakeNinja - CMakePythonPackage - Cargo - CargoPythonBundle - CargoPythonPackage - CmdCp - Conda - ConfigureMake - ConfigureMakePythonPackage - CrayToolchain - FortranPythonPackage - GoPackage - IntelBase - JAR - JuliaBundle - JuliaPackage - MakeCp - MesonNinja - ModuleRC - OCamlPackage - OctavePackage - PackedBinary - PerlBundle - PerlModule - PythonBundle - PythonPackage - RPackage - Rpm - RubyGem - SCons - SystemCompiler - SystemMPI - Tarball - Toolchain - VSCPythonPackage - VersionIndependentPythonPackage - Waf
"},{"location":"version-specific/generic-easyblocks/#binariestarball","title":"Support for installing software that comes in binary form. Just copy the sources to the install dir, or use the specified install command.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-binary-easyblock","title":"Extra easyconfig parameters specific to We use the default CMakeMake implementation, and use install_step from MakeCp.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-cmakemakecp-easyblock","title":"Extra easyconfig parameters specific to Support for configuring with CMake, building and installing with MesonNinja.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-cmakeninja-easyblock","title":"Extra easyconfig parameters specific to Build a Python package and module with cmake.
Some packages use cmake to first build and install C Python packages and then put the Python package in lib/pythonX.Y/site-packages.
We use the default CMake implementation, and use make_module_extra from PythonPackage to generate a module file which sets the PYTHONPATH.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-cmakepythonpackage-easyblock","title":"Extra easyconfig parameters specific to Builds just like PythonBundle with setup for Rust and crates from Cargo easyblock
The cargo init step will set up the environment variables for rustc and vendor sources but all the build steps are triggered like normal.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-cargopythonbundle-easyblock","title":"Extra easyconfig parameters specific to Build a Python package with setup from Cargo but build/install step from PythonPackage
The cargo init step will set up the environment variables for rustc and vendor sources but all the build steps are triggered via normal PythonPackage steps like normal.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-cargopythonpackage-easyblock","title":"Extra easyconfig parameters specific to Software with no configure, no make, and no make install step. Just run the specified command for all sources, and copy specified files to the install dir
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-cmdcp-easyblock","title":"Extra easyconfig parameters specific to Support for installing software using 'conda'.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-conda-easyblock","title":"Extra easyconfig parameters specific to Support for building and installing applications with configure/make/make install
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-configuremake-easyblock","title":"Extra easyconfig parameters specific to Builds and installs a Go package, and provides a dedicated module file.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-gopackage-easyblock","title":"Extra easyconfig parameters specific to Support for installing JAR files.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-jar-easyblock","title":"Extra easyconfig parameters specific to Bundle of JuliaPackages: install Julia packages as extensions in a bundle Defines custom sanity checks and module environment
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-juliabundle-easyblock","title":"Extra easyconfig parameters specific to Builds and installs Julia Packages.
Julia environment setup during installation: - initialize new Julia environment in 'environments' subdir in installation directory - remove paths in user depot '~/.julia' from DEPOT_PATH and LOAD_PATH - put installation directory as top DEPOT_PATH, the target depot for installations with Pkg - put installation environment as top LOAD_PATH, needed to precompile installed packages - add Julia packages found in dependencies of the easyconfig to installation environment, needed for Pkg to be aware of those packages and not install them again - add newly installed Julia packages to installation environment (automatically done by Pkg)
Julia environment setup on module load: User depot and its shared environment for this version of Julia are kept as top paths of DEPOT_PATH and LOAD_PATH respectively. This ensures that the user can keep using its own environment after loading JuliaPackage modules, installing additional software on its personal depot while still using packages provided by the module. Effectively, this translates to: - append installation directory to list of DEPOT_PATH, only really needed to load artifacts (JLL packages) - append installation Project.toml file to list of LOAD_PATH, needed to load packages with using command
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-juliapackage-easyblock","title":"Extra easyconfig parameters specific to Software with no configure and no make install step.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-makecp-easyblock","title":"Extra easyconfig parameters specific to Support for building and installing software with 'meson' and 'ninja'.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-mesonninja-easyblock","title":"Extra easyconfig parameters specific to Builds and installs OCaml packages using OPAM package manager.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-ocamlpackage-easyblock","title":"Extra easyconfig parameters specific to Builds and installs Octave extension toolboxes.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-octavepackage-easyblock","title":"Extra easyconfig parameters specific to Support for installing packed binary software. Just unpack the sources in the install dir
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-packedbinary-easyblock","title":"Extra easyconfig parameters specific to Builds and installs a Perl module, and can provide a dedicated module file.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-perlmodule-easyblock","title":"Extra easyconfig parameters specific to Bundle of PythonPackages: install Python packages as extensions in a bundle Defines custom sanity checks and module environment
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-pythonbundle-easyblock","title":"Extra easyconfig parameters specific to Builds and installs a Python package, and provides a dedicated module file.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-pythonpackage-easyblock","title":"Extra easyconfig parameters specific to Install an R package as a separate module, or as an extension.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-rpackage-easyblock","title":"Extra easyconfig parameters specific to Support for installing RPM files.
Builds and installs Ruby Gems.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-rubygem-easyblock","title":"Extra easyconfig parameters specific to Support for building/installing with SCons.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-scons-easyblock","title":"Extra easyconfig parameters specific to Support for generating a module file for the system compiler with specified name.
The compiler is expected to be available in $PATH, required libraries are assumed to be readily available.
Specifying 'system' as a version leads to using the derived compiler version in the generated module; if an actual version is specified, it is checked against the derived version of the system compiler that was found.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-systemcompiler-easyblock","title":"Extra easyconfig parameters specific to Support for generating a module file for the system mpi with specified name.
The mpi compiler is expected to be available in $PATH, required libraries are assumed to be readily available.
Specifying 'system' as a version leads to using the derived mpi version in the generated module; if an actual version is specified, it is checked against the derived version of the system mpi that was found.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-systemmpi-easyblock","title":"Extra easyconfig parameters specific to Precompiled software supplied as a tarball: will unpack binary and copy it to the install dir
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-tarball-easyblock","title":"Extra easyconfig parameters specific to Compiler toolchain easyblock: nothing to install, just generate module file.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-toolchain-easyblock","title":"Extra easyconfig parameters specific to Support for install VSC Python packages.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-vscpythonpackage-easyblock","title":"Extra easyconfig parameters specific to Support for building/installing python packages without requiring a specific python package.
"},{"location":"version-specific/generic-easyblocks/#extra-easyconfig-parameters-specific-to-versionindependentpythonpackage-easyblock","title":"Extra easyconfig parameters specific to -
build_step - Build with ./waf build
-
configure_step - Configure with ./waf configure --prefix=
-
install_step - Install with ./waf install
"},{"location":"version-specific/toolchain-opts/","title":"Available toolchain options (by toolchain)","text":"(see also eb --avail-toolchain-opts <tcname> )
cgmpich - cgmpolf - cgmvapich2 - cgmvolf - cgompi - cgoolf - ClangGCC - CrayCCE - CrayGNU - CrayIntel - CrayPGI - FCC - ffmpi - foss - fosscuda - Fujitsu - GCC - GCCcore - gcccuda - gfbf - gimkl - gimpi - gimpic - giolf - giolfc - gmacml - gmkl - gmklc - gmpflf - gmpich2 - gmpich - gmpit - gmpolf - gmvapich2 - gmvolf - GNU - goalf - gobff - goblf - gofbf - golf - golfc - gomkl - gomklc - gompi - gompic - goolf - goolfc - gpsmpi - gpsolf - gqacml - gsmpi - gsolf - iccifort - iccifortcuda - ictce - ifbf - iibff - iimkl - iimklc - iimpi - iimpic - iiqmpi - impich - impmkl - intel-compilers - intel-para - intel - intelcuda - iofbf - iomkl - iomklc - iompi - iompic - ipsmpi - iqacml - ismkl - NVHPC - nvofbf - nvompi - nvompic - nvpsmpi - nvpsmpic - PGI - pmkl - pomkl - pompi - system - xlcxlf - xlmpich2 - xlmpich - xlmvapich2 - xlompi
"},{"location":"version-specific/toolchain-opts/#cgmpich","title":"cgmpich","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-cgmpich-toolchain","title":"Available options for cgmpich toolchain","text":"option description default 32bit Compile 32bit target False basic-block-vectorize Basic block vectorization False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False extra_cflags Specify extra CFLAGS options. None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. 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None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. 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None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. None i8 Integers are 8 byte integers False ieee Adhere to IEEE-754 rules False loop-vectorize Loop vectorization False loose Loose precision False lowopt Low compiler optimizations False noopt Disable compiler optimizations False openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations True packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False usempi Use MPI compiler as default compiler False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output False veryloose Very loose precision False"},{"location":"version-specific/toolchain-opts/#cgmvolf","title":"cgmvolf","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-cgmvolf-toolchain","title":"Available options for cgmvolf toolchain","text":"option description default 32bit Compile 32bit target False basic-block-vectorize Basic block vectorization False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False extra_cflags Specify extra CFLAGS options. None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. 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None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. 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None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. None i8 Integers are 8 byte integers False ieee Adhere to IEEE-754 rules False loop-vectorize Loop vectorization False loose Loose precision False lowopt Low compiler optimizations False noopt Disable compiler optimizations False openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations True packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False usempi Use MPI compiler as default compiler False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output False veryloose Very loose precision False"},{"location":"version-specific/toolchain-opts/#clanggcc","title":"ClangGCC","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-clanggcc-toolchain","title":"Available options for ClangGCC toolchain","text":"option description default 32bit Compile 32bit target False basic-block-vectorize Basic block vectorization False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False extra_cflags Specify extra CFLAGS options. None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. None i8 Integers are 8 byte integers False ieee Adhere to IEEE-754 rules False loop-vectorize Loop vectorization False loose Loose precision False lowopt Low compiler optimizations False noopt Disable compiler optimizations False openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations True packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output False veryloose Very loose precision False"},{"location":"version-specific/toolchain-opts/#craycce","title":"CrayCCE","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-craycce-toolchain","title":"Available options for CrayCCE toolchain","text":"option description default 32bit Compile 32bit target False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False dynamic Generate dynamically linked executable True extra_cflags Specify extra CFLAGS options. None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. None i8 Integers are 8 byte integers False ieee Adhere to IEEE-754 rules False loose Loose precision False lowopt Low compiler optimizations False mpich-mt Directs the driver to link in an alternate version of the Cray-MPICH library which provides fine-grained multi-threading support to applications that perform MPI operations within threaded regions. False noopt Disable compiler optimizations False openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations False packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False usempi Use MPI compiler as default compiler False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output True veryloose Very loose precision False"},{"location":"version-specific/toolchain-opts/#craygnu","title":"CrayGNU","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-craygnu-toolchain","title":"Available options for CrayGNU toolchain","text":"option description default 32bit Compile 32bit target False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False dynamic Generate dynamically linked executable True extra_cflags Specify extra CFLAGS options. None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. None i8 Integers are 8 byte integers False ieee Adhere to IEEE-754 rules False loose Loose precision False lowopt Low compiler optimizations False mpich-mt Directs the driver to link in an alternate version of the Cray-MPICH library which provides fine-grained multi-threading support to applications that perform MPI operations within threaded regions. False noopt Disable compiler optimizations False openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations False packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False usempi Use MPI compiler as default compiler False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output True veryloose Very loose precision False"},{"location":"version-specific/toolchain-opts/#crayintel","title":"CrayIntel","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-crayintel-toolchain","title":"Available options for CrayIntel toolchain","text":"option description default 32bit Compile 32bit target False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False dynamic Generate dynamically linked executable True extra_cflags Specify extra CFLAGS options. None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. None i8 Integers are 8 byte integers False ieee Adhere to IEEE-754 rules False loose Loose precision False lowopt Low compiler optimizations False mpich-mt Directs the driver to link in an alternate version of the Cray-MPICH library which provides fine-grained multi-threading support to applications that perform MPI operations within threaded regions. False noopt Disable compiler optimizations False openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations False packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False usempi Use MPI compiler as default compiler False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output True veryloose Very loose precision False"},{"location":"version-specific/toolchain-opts/#craypgi","title":"CrayPGI","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-craypgi-toolchain","title":"Available options for CrayPGI toolchain","text":"option description default 32bit Compile 32bit target False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False dynamic Generate dynamically linked executable True extra_cflags Specify extra CFLAGS options. None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. None i8 Integers are 8 byte integers False ieee Adhere to IEEE-754 rules False loose Loose precision False lowopt Low compiler optimizations False mpich-mt Directs the driver to link in an alternate version of the Cray-MPICH library which provides fine-grained multi-threading support to applications that perform MPI operations within threaded regions. False noopt Disable compiler optimizations False openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations False packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False usempi Use MPI compiler as default compiler False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output True veryloose Very loose precision False"},{"location":"version-specific/toolchain-opts/#fcc","title":"FCC","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-fcc-toolchain","title":"Available options for FCC toolchain","text":"option description default 32bit Compile 32bit target False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False extra_cflags Specify extra CFLAGS options. None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. None i8 Integers are 8 byte integers False ieee Adhere to IEEE-754 rules False loose Loose precision False lowopt Low compiler optimizations False noopt Disable compiler optimizations False openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations True packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output False veryloose Very loose precision False"},{"location":"version-specific/toolchain-opts/#ffmpi","title":"ffmpi","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-ffmpi-toolchain","title":"Available options for ffmpi toolchain","text":"option description default 32bit Compile 32bit target False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False extra_cflags Specify extra CFLAGS options. None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. 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None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. 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None i8 Integers are 8 byte integers False ieee Adhere to IEEE-754 rules False intel-static Link Intel provided libraries statically False loose Loose precision False lowopt Low compiler optimizations False no-icc Don't set Intel specific macros False noopt Disable compiler optimizations False oneapi Use oneAPI compilers icx/icpx/ifx instead of classic compilers None oneapi_c_cxx Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer) None oneapi_fortran Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler (auto-enabled for Intel compilers version 2024.0.0, or newer) None openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations True packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False usempi Use MPI compiler as default compiler False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output False veryloose Very loose precision False"},{"location":"version-specific/toolchain-opts/#iimpic","title":"iimpic","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-iimpic-toolchain","title":"Available options for iimpic toolchain","text":"option description default 32bit Compile 32bit target False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False error-unknown-option Error instead of warning for unknown options False extra_cflags Specify extra CFLAGS options. 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None i8 Integers are 8 byte integers False ieee Adhere to IEEE-754 rules False intel-static Link Intel provided libraries statically False loose Loose precision False lowopt Low compiler optimizations False no-icc Don't set Intel specific macros False noopt Disable compiler optimizations False openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations True packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False usempi Use MPI compiler as default compiler False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output False veryloose Very loose precision False"},{"location":"version-specific/toolchain-opts/#intel","title":"intel","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-intel-toolchain","title":"Available options for intel toolchain","text":"option description default 32bit Compile 32bit target False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False error-unknown-option Error instead of warning for unknown options False extra_cflags Specify extra CFLAGS options. 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None i8 Integers are 8 byte integers False ieee Adhere to IEEE-754 rules False intel-static Link Intel provided libraries statically False loose Loose precision False lowopt Low compiler optimizations False no-icc Don't set Intel specific macros False noopt Disable compiler optimizations False oneapi Use oneAPI compilers icx/icpx/ifx instead of classic compilers None oneapi_c_cxx Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer) None oneapi_fortran Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler (auto-enabled for Intel compilers version 2024.0.0, or newer) None openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations True packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False usempi Use MPI compiler as default compiler False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output False veryloose Very loose precision False"},{"location":"version-specific/toolchain-opts/#intelcuda","title":"intelcuda","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-intelcuda-toolchain","title":"Available options for intelcuda toolchain","text":"option description default 32bit Compile 32bit target False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False error-unknown-option Error instead of warning for unknown options False extra_cflags Specify extra CFLAGS options. 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None i8 Integers are 8 byte integers False ieee Adhere to IEEE-754 rules False intel-static Link Intel provided libraries statically False loose Loose precision False lowopt Low compiler optimizations False no-icc Don't set Intel specific macros False noopt Disable compiler optimizations False openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations True packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False usempi Use MPI compiler as default compiler False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output False veryloose Very loose precision False"},{"location":"version-specific/toolchain-opts/#iofbf","title":"iofbf","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-iofbf-toolchain","title":"Available options for iofbf toolchain","text":"option description default 32bit Compile 32bit target False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False error-unknown-option Error instead of warning for unknown options False extra_cflags Specify extra CFLAGS options. 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None i8 Integers are 8 byte integers False ieee Adhere to IEEE-754 rules False intel-static Link Intel provided libraries statically False loose Loose precision False lowopt Low compiler optimizations False no-icc Don't set Intel specific macros False noopt Disable compiler optimizations False oneapi Use oneAPI compilers icx/icpx/ifx instead of classic compilers None oneapi_c_cxx Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer) None oneapi_fortran Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler (auto-enabled for Intel compilers version 2024.0.0, or newer) None openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations True packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False usempi Use MPI compiler as default compiler False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output False veryloose Very loose precision False"},{"location":"version-specific/toolchain-opts/#iomkl","title":"iomkl","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-iomkl-toolchain","title":"Available options for iomkl toolchain","text":"option description default 32bit Compile 32bit target False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False error-unknown-option Error instead of warning for unknown options False extra_cflags Specify extra CFLAGS options. 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None i8 Integers are 8 byte integers False ibm-static Link IBM XL provided libraries statically False ieee Adhere to IEEE-754 rules False loose Loose precision False lowopt Low compiler optimizations False noopt Disable compiler optimizations False openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations True packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False usempi Use MPI compiler as default compiler False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output False veryloose Very loose precision False"},{"location":"version-specific/toolchain-opts/#xlompi","title":"xlompi","text":""},{"location":"version-specific/toolchain-opts/#available-options-for-xlompi-toolchain","title":"Available options for xlompi toolchain","text":"option description default 32bit Compile 32bit target False cciscxx Use CC as CXX False cstd Specify C standard None debug Enable debug False defaultopt Default compiler optimizations False defaultprec Default precision False error-unknown-option Error instead of warning for unknown options False extra_cflags Specify extra CFLAGS options. None extra_cxxflags Specify extra CXXFLAGS options. None extra_f90flags Specify extra F90FLAGS options. None extra_fcflags Specify extra FCFLAGS options. None extra_fflags Specify extra FFLAGS options. None i8 Integers are 8 byte integers False ibm-static Link IBM XL provided libraries statically False ieee Adhere to IEEE-754 rules False loose Loose precision False lowopt Low compiler optimizations False noopt Disable compiler optimizations False openmp Enable OpenMP False opt High compiler optimizations False optarch Enable architecture optimizations True packed-linker-options Pack the linker options as comma separated list False pic Use PIC False precise High precision False r8 Real is 8 byte real False rpath Use RPATH wrappers when --rpath is enabled in EasyBuild configuration True shared Build shared library False static Build static library False strict Strict (highest) precision False unroll Unroll loops False usempi Use MPI compiler as default compiler False vectorize Enable compiler auto-vectorization, default except for noopt and lowopt None verbose Verbose output False veryloose Very loose precision False"},{"location":"version-specific/toolchains/","title":"List of known toolchains","text":"Name Compiler(s) MPI Linear algebra FFT cgmpich Clang, GCC MPICH (none) (none) cgmpolf Clang, GCC MPICH OpenBLAS, ScaLAPACK FFTW cgmvapich2 Clang, GCC MVAPICH2 (none) (none) cgmvolf Clang, GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW cgompi Clang, GCC OpenMPI (none) (none) cgoolf Clang, GCC OpenMPI OpenBLAS, ScaLAPACK FFTW ClangGCC Clang, GCC (none) (none) (none) CrayCCE PrgEnv-cray cray-mpich cray-libsci (none) CrayGNU PrgEnv-gnu cray-mpich cray-libsci (none) CrayIntel PrgEnv-intel cray-mpich cray-libsci (none) CrayPGI PrgEnv-pgi cray-mpich cray-libsci (none) FCC lang (none) (none) (none) ffmpi FCC (none) (none) (none) foss GCC OpenMPI OpenBLAS, ScaLAPACK FFTW fosscuda GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW Fujitsu FCC (none) (none) FFTW GCC GCC (none) (none) (none) GCCcore GCCcore (none) (none) (none) gcccuda GCC, CUDA (none) (none) (none) gfbf GCC (none) FlexiBLAS FFTW gimkl GCC impi imkl imkl gimpi GCC impi (none) (none) gimpic GCC, CUDA impi (none) (none) giolf GCC impi OpenBLAS, ScaLAPACK FFTW giolfc GCC, CUDA impi OpenBLAS, ScaLAPACK FFTW gmacml GCC MVAPICH2 ACML, ScaLAPACK FFTW gmkl GCC (none) imkl imkl gmklc GCC, CUDA (none) imkl imkl gmpflf GCC MPICH FlexiBLAS, ScaLAPACK FFTW gmpich GCC MPICH (none) (none) gmpich2 GCC MPICH2 (none) (none) gmpit GCC MPItrampoline (none) (none) gmpolf GCC MPICH OpenBLAS, ScaLAPACK FFTW gmvapich2 GCC MVAPICH2 (none) (none) gmvolf GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW GNU GCC (none) (none) (none) goalf GCC OpenMPI ATLAS, ScaLAPACK FFTW gobff GCC OpenMPI BLIS, libFLAME, ScaLAPACK FFTW goblf GCC OpenMPI BLIS, LAPACK, ScaLAPACK FFTW gofbf GCC OpenMPI FlexiBLAS, ScaLAPACK FFTW golf GCC (none) OpenBLAS FFTW golfc GCC, CUDA (none) OpenBLAS FFTW gomkl GCC OpenMPI imkl imkl gomklc GCC, CUDA OpenMPI imkl imkl gompi GCC OpenMPI (none) (none) gompic GCC, CUDA OpenMPI (none) (none) goolf GCC OpenMPI OpenBLAS, ScaLAPACK FFTW goolfc GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW gpsmpi GCC psmpi (none) (none) gpsolf GCC psmpi OpenBLAS, ScaLAPACK FFTW gqacml GCC QLogicMPI ACML, ScaLAPACK FFTW gsmpi GCC SpectrumMPI (none) (none) gsolf GCC SpectrumMPI OpenBLAS, ScaLAPACK FFTW iccifort icc, ifort (none) (none) (none) iccifortcuda icc, ifort, CUDA (none) (none) (none) ictce icc, ifort impi imkl imkl ifbf intel-compilers (none) FlexiBLAS FFTW iibff icc, ifort impi BLIS, libFLAME, ScaLAPACK FFTW iimkl icc, ifort (none) imkl imkl iimklc icc, ifort (none) imkl imkl iimpi icc, ifort impi (none) (none) iimpic icc, ifort, CUDA impi (none) (none) iiqmpi icc, ifort QLogicMPI (none) (none) impich icc, ifort MPICH (none) (none) impmkl icc, ifort MPICH imkl imkl intel icc, ifort impi imkl imkl intel-compilers intel-compilers (none) (none) (none) intel-para icc, ifort psmpi imkl imkl intelcuda icc, ifort, CUDA impi imkl imkl iofbf icc, ifort OpenMPI FlexiBLAS, ScaLAPACK FFTW iomkl icc, ifort OpenMPI imkl imkl iomklc icc, ifort, CUDA OpenMPI imkl imkl iompi icc, ifort OpenMPI (none) (none) iompic icc, ifort, CUDA OpenMPI (none) (none) ipsmpi icc, ifort psmpi (none) (none) iqacml icc, ifort QLogicMPI ACML, ScaLAPACK FFTW ismkl icc, ifort MPICH2 imkl imkl NVHPC NVHPC (none) (none) (none) nvofbf NVHPC OpenMPI FlexiBLAS, ScaLAPACK FFTW nvompi NVHPC OpenMPI (none) (none) nvompic NVHPC OpenMPI (none) (none) nvpsmpi NVHPC psmpi (none) (none) nvpsmpic NVHPC psmpi (none) (none) PGI PGI (none) (none) (none) pmkl PGI (none) imkl imkl pomkl PGI OpenMPI imkl imkl pompi PGI OpenMPI (none) (none) system (none) (none) (none) (none) xlcxlf xlc, xlf (none) (none) (none) xlmpich xlc, xlf MPICH (none) (none) xlmpich2 xlc, xlf MPICH2 (none) (none) xlmvapich2 xlc, xlf MVAPICH2 (none) (none) xlompi xlc, xlf OpenMPI (none) (none) (see also eb --list-toolchains )
"},{"location":"version-specific/supported-software/","title":"List of supported software","text":"(quick links: 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
EasyBuild supports 3670 different software packages (incl. toolchains, bundles):
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- a
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- behave
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- BGC-Bayesian-genomic-clines
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- binutils
- Bio-DB-HTS
- Bio-EUtilities
- Bio-FeatureIO
- Bio-SamTools
- Bio-SearchIO-hmmer
- bioawk
- biobakery-workflows
- biobambam2
- biogeme
- biom-format
- biomart-perl
- BioPerl
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- BioServices
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- BOINC
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- BoltzTraP2
- Bonito
- Bonmin
- Bonnie++
- Boost
- Boost.MPI
- Boost.Python
- Boost.Python-NumPy
- boost_histogram
- BOPTEST
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- Bottleneck
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- BSseeker2
- btllib
- BuDDy
- BUFRLIB
- build
- buildenv
- buildingspy
- Bullet
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- BUStools
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- bwa-meth
- bwakit
- bwidget
- BWISE
- bx-python
- BXH_XCEDE_TOOLS
- byacc
- byobu
- bzip2
- c
- c-ares
- C3D
- cadaver
- CaDiCaL
- CAFE5
- Caffe
- cairo
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- Calcam
- CalculiX-CrunchiX
- Calendrical
- Calib
- CAMPARI
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- Canvas
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- CapnProto
- captum
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- Cartopy
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- CASPR
- Cassiopeia
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- CastXML
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- CatBoost
- Catch2
- category_encoders
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- cDNA_Cupcake
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- Check
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- CheckM-Database
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- Chemaxon-Marvin
- chemprop
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- Chimera
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- CIRIquant
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- Demystify
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- dx-toolkit
- dxpy
- DyMat
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- E-ANTIC
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- ea-utils
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- easel
- EasyBuild
- EasyMocap
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- EDirect
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- EIGENSOFT
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- Elmer
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- elprep
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- EMAN2
- EMBOSS
- Embree
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- EnergyPlus
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- EVcouplings
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- EveryBeam
- EvidentialGene
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- ExaBayes
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- Excel-Writer-XLSX
- ExifTool
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- Exonerate
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- ExtremeLy
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- fastahack
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- FIGARO
- FigureGen
- Fiji
- file
- filevercmp
- Filtlong
- find_circ
- finder
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- findutils
- fineRADstructure
- fineSTRUCTURE
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- Firefox
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- FireWorks
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- FIX
- fixesproto
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- freebayes
- FreeFEM
- FreeFem++
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- GRASP
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- i
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- IMAGE
- imagecodecs
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- imake
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- InChI
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- Inferelator
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- INTEGRATE
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- j
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- k
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- m
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- o
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- p
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- p4-phylogenetics
- p4est
- p4vasp
- p7zip
- packmol
- PAGAN2
- pagmo
- pairsnp
- PAL2NAL
- paladin
- PALEOMIX
- PAML
- panaroo
- pandapower
- pandas
- pandas-datareader
- PANDAseq
- Pandoc
- Panedr
- Pango
- pangolin
- panito
- PAPI
- parallel
- parallel-fastq-dump
- Parallel-Hashmap
- ParallelIO
- parameterized
- paramiko
- parasail
- Paraver
- ParaView
- Parcels
- PARI-GP
- ParmEd
- ParMETIS
- ParMGridGen
- Parsl
- PartitionFinder
- PASA
- pasta
- PaStiX
- pastml
- patch
- patchelf
- path.py
- PAUP
- pauvre
- pbbam
- pbcopper
- pbdagcon
- pbipa
- pblat
- pbmm2
- pbs_python
- PBSuite
- PBZIP2
- PCAngsd
- PCC
- PCL
- PCMSolver
- PCRaster
- PCRE
- PCRE2
- pdf2docx
- PDM
- pdsh
- PDT
- peakdetect
- PEAR
- PEcAn
- PennCNV
- PEPT
- Percolator
- Perl
- perl-app-cpanminus
- Perl-bundle-CPAN
- Perl4-CoreLibs
- Perseus
- PEST++
- PETSc
- petsc4py
- PfamScan
- PFFT
- pfind
- pftoolsV3
- pFUnit
- PGDSpider
- PGI
- PGPLOT
- PHANOTATE
- Phantompeakqualtools
- PHASE
- phasius
- PHAST
- Phenoflow
- PheWAS
- PheWeb
- Philosopher
- PhiPack
- PHLAT
- phonemizer
- phono3py
- phonopy
- photontorch
- phototonic
- PHYLIP
- PhyloBayes-MPI
- phylokit
- phylonaut
- PhyloPhlAn
- phyluce
- PhyML
- phyx
- picard
- PICI-LIGGGHTS
- PICRUSt2
- pigz
- PIL
- PileOMeth
- Pillow
- Pillow-SIMD
- Pilon
- PIMS
- Pindel
- Pingouin
- Pint
- pip
- PIPITS
- PIRATE
- pIRS
- Pisces
- piSvM
- piSvM-JSC
- pixman
- pizzly
- pkg-config
- pkgconf
- pkgconfig
- PLAMS
- planarity
- plantcv
- plantri
- PlaScope
- PlasmaPy
- PLAST
- Platanus
- Platypus
- Platypus-Opt
- plc
- PLINK
- plinkliftover
- plinkQC
- PLINKSEQ
- plmc
- plot1cell
- Ploticus
- plotly
- plotly-orca
- plotly.py
- plotutils
- PLplot
- PLUMED
- PLY
- PMIx
- pmt
- pmx
- PnetCDF
- pocl
- pod5-file-format
- poetry
- polars
- polymake
- pomkl
- pompi
- poppler
- poppunk
- popscle
- popt
- Porechop
- porefoam
- poretools
- PortAudio
- Portcullis
- PortMidi
- Postgres-XL
- PostgreSQL
- POT
- POV-Ray
- powerlaw
- pp-sketchlib
- PPanGGOLiN
- PPfold
- ppl
- pplacer
- pplpy
- PRANK
- PRC
- preCICE
- premailer
- PREQUAL
- preseq
- presto
- PretextMap
- pretty-yaml
- primecount
- primecountpy
- Primer3
- PRINSEQ
- printproto
- PRISMS-PF
- ProbABEL
- ProBiS
- prodigal
- ProFit
- PROJ
- ProjectQ
- prokka
- prompt-toolkit
- proovread
- propy
- ProteinMPNN
- Proteinortho
- ProtHint
- protobuf
- protobuf-python
- protozero
- PRRTE
- PRSice
- PSASS
- pscom
- PSI
- PSI4
- PsiCLASS
- PSIPRED
- PSM2
- psmc
- psmpi
- psmpi2
- PSolver
- PSORTb
- psrecord
- pstoedit
- psutil
- psycopg
- psycopg2
- ptemcee
- PTESFinder
- pubtcrs
- pugixml
- pullseq
- PuLP
- purge_dups
- pv
- py
- py-aiger
- py-aiger-bdd
- py-c3d
- py-cpuinfo
- py3Dmol
- pyABC
- PyAEDT
- PyAMG
- PyAPS3
- PyAV
- pybedtools
- PyBEL
- PyBerny
- pyBigWig
- pybind11
- pybind11-stubgen
- pybinding
- PyBioLib
- PyBullet
- PyCairo
- PyCalib
- pyccel
- PyCharm
- PyCheMPS2
- Pychopper
- PyCifRW
- PyClone
- pycma
- pycocotools
- pycodestyle
- PyCogent
- pycoQC
- pycubescd
- PyCUDA
- PycURL
- PyDamage
- pydantic
- PyDatastream
- pydicom
- pydicom-seg
- pydlpoly
- pydot
- pyEGA3
- pyenchant
- PyEVTK
- PyEXR
- pyFAI
- pyfaidx
- pyfasta
- PyFFmpeg
- pyFFTW
- pyfits
- PyFMI
- PyFoam
- PyFR
- PyFrag
- pyGAM
- pygame
- pygccxml
- pyGenomeTracks
- PyGEOS
- pyGIMLi
- Pygments
- pygmo
- PyGObject
- pygraphviz
- pygrib
- PyGTK
- PyGTS
- PyGWAS
- pyhdf
- PyHMMER
- PyImageJ
- PyInstaller
- pyiron
- Pyke3
- pylift
- Pylint
- pylipid
- pyMannKendall
- pymatgen
- pymatgen-db
- pymbar
- pyMBE
- PyMC
- PyMC3
- pymca
- pymemcache
- PyMOL
- PyNAST
- pyobjcryst
- PyOD
- pyodbc
- Pyomo
- PyOpenCL
- PyOpenGL
- pyparsing
- pyperf
- pyplusplus
- pypmt
- PYPOWER
- pyproj
- PyPSA
- PyPy
- pyqstem
- PyQt
- PyQt-builder
- PyQt5
- PyQtGraph
- pyradiomics
- PyRe
- PyRETIS
- pyringe
- pyro-api
- pyro-ppl
- Pyro4
- PyRosetta
- Pysam
- pysamstats
- PySAT
- pyScaf
- pySCENIC
- PySCF
- pyseer
- pysheds
- pyshp
- PySide2
- PySINDy
- pyslim
- pysndfx
- Pysolar
- pyspoa
- pysqlite
- PyStan
- pystencils
- pysteps
- pystran
- PyTables
- PyTensor
- pytesseract
- pytest
- pytest-benchmark
- pytest-cpp
- pytest-flakefinder
- pytest-rerunfailures
- pytest-shard
- pytest-workflow
- pytest-xdist
- pythermalcomfort
- PYTHIA
- Python
- python-blosc
- Python-bundle
- Python-bundle-PyPI
- python-casacore
- python-docx
- python-elf
- python-hl7
- python-igraph
- python-irodsclient
- python-isal
- python-Levenshtein
- python-libsbml
- python-louvain
- python-mujoco
- python-parasail
- python-telegram-bot
- python-weka-wrapper3
- python-xxhash
- pythran
- PyTorch
- pytorch-3dunet
- PyTorch-bundle
- pytorch-CycleGAN-pix2pix
- PyTorch-Geometric
- PyTorch-Ignite
- PyTorch-Image-Models
- PyTorch-Lightning
- PyTorch3D
- PyTorchVideo
- PyVCF
- PyVCF3
- PyVista
- pyWannier90
- PyWavelets
- PyWBGT
- pyXDF
- PyYAML
- PyZMQ
- q
- q2-krona
- Q6
- QCA
- qcat
- QCG-PilotJob
- qcint
- QCxMS
- QD
- QDD
- QEMU
- qforce
- QGIS
- Qhull
- QIIME
- QIIME2
- Qiskit
- QJson
- qmflows
- QML
- qnorm
- qpth
- qrupdate
- QScintilla
- Qt
- Qt5
- Qt5Webkit
- Qt6
- Qtconsole
- QtKeychain
- QTLtools
- qtop
- QtPy
- Qualimap
- Quandl
- QuantumESPRESSO
- QUAST
- QuaZIP
- QuickFF
- QuickPIC
- QuickTree
- Quip
- Quorum
- QuPath
- QuTiP
- Qwt
- QwtPolar
- r
- R
- R-bundle-Bioconductor
- R-bundle-CRAN
- R-INLA
- R-keras
- R-MXM
- R-opencv
- R-tesseract
- R-transport
- R2jags
- Racon
- radeontop
- radian
- RaGOO
- Ragout
- RagTag
- rampart
- randfold
- randrproto
- rankwidth
- rapidcsv
- RapidJSON
- rapidNJ
- rapidtide
- RAPSearch2
- Raptor
- Rascaf
- RASPA2
- Rasqal
- rasterio
- rasterstats
- Ratatosk
- Raven
- RAxML
- RAxML-NG
- Ray-assembler
- Ray-project
- Raysect
- RBFOpt
- RCall
- rclone
- Rcorrector
- RcppGSL
- rCUDA
- RDFlib
- RDKit
- RDP-Classifier
- RE2
- re2c
- Reads2snp
- Reapr
- ReaxFF
- RECON
- Red
- Redis
- redis-py
- Redland
- Redundans
- ReFrame
- Regenie
- regionmask
- RegTools
- Relate
- RELION
- remake
- ReMatCh
- REMORA
- renderproto
- RepastHPC
- RepeatMasker
- RepeatModeler
- RepeatScout
- request
- requests
- RERconverge
- ResistanceGA
- resolos
- Restrander
- rethinking
- retworkx
- RevBayes
- RFdiffusion
- rgdal
- rgeos
- Rgurobi
- rhdf5
- RHEIA
- RheoTool
- Rhodium
- rickflow
- RInChI
- rioxarray
- ripunzip
- rising
- Rivet
- rjags
- RLCard
- rmarkdown
- Rmath
- rMATS-long
- rMATS-turbo
- RMBlast
- RNA-Bloom
- RNA-SeQC
- RNAclust
- RNAcode
- RNAIndel
- RNAmmer
- rnamotif
- rnaQUAST
- RNAz
- RnBeads
- Roary
- ROCm
- rocm-cmake
- ROCm-CompilerSupport
- rocm-smi
- rocminfo
- ROCR-Runtime
- ROCT-Thunk-Interface
- ROI_PAC
- ROME
- ROOT
- root_numpy
- rootpy
- Rosetta
- rpmrebuild
- RPostgreSQL
- rpy2
- RQGIS3
- RSEM
- RSeQC
- RStan
- rstanarm
- RStudio-Server
- RTG-Tools
- Rtree
- ruamel.yaml
- Ruby
- Ruby-Tk
- ruffus
- ruptures
- Rust
- rustworkx
- s
- S-Lang
- s3fs
- S4
- Sabre
- safestringlib
- Safetensors
- SAGE
- Sagemath
- Sailfish
- SALib
- Salmon
- SALMON-TDDFT
- Sambamba
- samblaster
- Samcef
- samclip
- samplot
- SAMtools
- sansa
- SAP
- SAS
- Satsuma2
- savvy
- Saxon-HE
- SBCL
- sbt
- ScaFaCoS
- ScaLAPACK
- Scalasca
- SCALCE
- Scalene
- scanpy
- scArches
- scCODA
- scCustomize
- sceasy
- SCENIC
- SCENICplus
- scFEA
- scGeneFit
- SCGid
- scGSVA
- scHiCExplorer
- Schrodinger
- scib
- scib-metrics
- sciClone
- ScientificPython
- scikit-allel
- scikit-bio
- scikit-build
- scikit-build-core
- scikit-cuda
- scikit-extremes
- scikit-image
- scikit-learn
- scikit-lego
- scikit-misc
- scikit-multilearn
- scikit-optimize
- scikit-plot
- scikit-uplift
- SCIP
- SCIPhI
- scipy
- SciPy-bundle
- SciTools-Iris
- SCnorm
- Scoary
- SCons
- SCOOP
- SCopeLoomR
- Score-P
- SCOTCH
- scp
- scPred
- Scrappie
- SCReadCounts
- scrublet
- scVelo
- scvi-tools
- Scythe
- SDCC
- SDL
- SDL2
- SDL2_gfx
- SDL2_image
- SDL2_mixer
- SDL2_ttf
- SDL_image
- SDSL
- sdsl-lite
- Seaborn
- SEACells
- SearchGUI
- SeaView
- SECAPR
- Seeder
- segemehl
- segment-anything
- segmentation-models
- segmentation-models-pytorch
- SeisSol
- SelEstim
- SELFIES
- SemiBin
- semla
- Sentence-Transformers
- SentencePiece
- sentinelsat
- sep
- SEPP
- Seq-Gen
- seq2HLA
- SeqAn
- SeqAn3
- SeqKit
- SeqLib
- Seqmagick
- SeqPrep
- seqtk
- Serf
- setuptools
- setuptools-rust
- Seurat
- SeuratData
- SeuratDisk
- SeuratWrappers
- sf
- sfftk
- Shannon
- SHAP
- shapAAR
- SHAPEIT
- SHAPEIT4
- Shapely
- SharedMeatAxe
- sharutils
- Shasta
- ShengBTE
- shift
- SHORE
- Short-Pair
- shovill
- shrinkwrap
- SHTns
- Sibelia
- SICER2
- sickle
- Siesta
- SignalP
- silhouetteRank
- silx
- simanneal
- simint
- SimNIBS
- SimPEG
- SIMPLE
- Simple-DFTD3
- SimpleElastix
- SimpleITK
- simpy
- Simstrat
- SimVascular
- Single-cell-python-bundle
- SingleM
- Singular
- sinto
- SiNVICT
- SIONlib
- SIP
- SIRIUS
- sirocco
- siscone
- SISSO
- SISSO++
- SKA2
- SKESA
- sketchmap
- skewer
- sklearn-pandas
- sklearn-som
- skorch
- sktime
- SlamDunk
- SLATEC
- SLEPc
- slepc4py
- sleuth
- slidingwindow
- SLiM
- slow5tools
- slurm-drmaa
- smafa
- smallgenomeutilities
- SMAP
- SMARTdenovo
- SMC++
- smfishHmrf
- smithwaterman
- Smoldyn
- smooth-topk
- SMRT-Link
- SMV
- snakemake
- SNAP
- SNAP-ESA
- SNAP-ESA-python
- SNAP-HMM
- SNAPE-pooled
- snaphu
- snappy
- Sniffles
- snippy
- snp-sites
- snpEff
- SNPhylo
- SNPomatic
- SOAPaligner
- SOAPdenovo-Trans
- SOAPdenovo2
- SOAPfuse
- socat
- SOCI
- SolexaQA++
- solo
- sonic
- SoPlex
- SoQt
- SortMeRNA
- SoupX
- SoX
- SoXt
- SpaceRanger
- Spack
- spaCy
- SPAdes
- spaln
- Spark
- sparse-neighbors-search
- sparsehash
- SpatialDE
- spatialreg
- spdlog
- SpectrA
- spectral.methods
- speech_tools
- SPEI
- spektral
- SpFFT
- spglib
- spglib-python
- Sphinx
- Sphinx-RTD-Theme
- SpiceyPy
- SpiecEasi
- spla
- SplAdder
- SPLASH
- SpliceMap
- split-seq
- splitRef
- SPM
- spoa
- SPOOLES
- SPOTPY
- SPRNG
- Spyder
- SQLAlchemy
- SQLite
- SqueezeMeta
- Squidpy
- SRA-Toolkit
- sradownloader
- SRPRISM
- SRST2
- SSAHA2
- SSN
- SSPACE_Basic
- SSW
- Stable-Baselines3
- STACEY
- Stack
- Stacks
- STAMP
- StaMPS
- Stampy
- STAR
- STAR-CCM+
- STAR-Fusion
- stardist
- starparser
- stars
- Stata
- Statistics-R
- statsmodels
- STEAK
- STIR
- stpipeline
- strace
- Strainberry
- STREAM
- strelka
- StringTie
- stripy
- STRique
- Structure
- Structure_threader
- STRUMPACK
- suave
- SuAVE-biomat
- submitit
- Subread
- subset-bam
- subunit
- Subversion
- suds
- SuiteSparse
- SUMACLUST
- SUMATRA
- SUMO
- SUNDIALS
- SunPy
- SuperLU
- SuperLU_DIST
- supermagic
- supernova
- SUPPA
- SURVIVOR
- SVclone
- SVDetect
- SVDquest
- SVDSS2
- SVG
- SVIM
- svist4get
- swarm
- SWASH
- SWAT+
- swifter
- SWIG
- SWIPE
- swissknife
- SymEngine
- SymEngine-python
- SYMMETRICA
- SYMPHONY
- sympy
- synapseclient
- synthcity
- SyRI
- sysbench
- Szip
- t
- T-Coffee
- t-SNE-CUDA
- tabix
- tabixpp
- taco
- TagDust
- TagLib
- Taiyaki
- TALON
- TALYS
- TAMkin
- tantan
- Tapenade
- task-spooler
- taxator-tk
- TBA
- tbb
- tbl2asn
- TCC
- Tcl
- TCLAP
- tcsh
- tdlib
- tecplot360ex
- TELEMAC-MASCARET
- Telescope
- Teneto
- tensorboard
- tensorboardX
- TensorFlow
- tensorflow-compression
- TensorFlow-Datasets
- TensorFlow-Graphics
- tensorflow-probability
- TensorRT
- terastructure
- termcolor
- Tesla-Deployment-Kit
- tesseract
- testpath
- TetGen
- TEToolkit
- TEtranscripts
- texinfo
- texlive
- Text-CSV
- TF-COMB
- TFEA
- Theano
- ThemisPy
- THetA
- thirdorder
- thurstonianIRT
- TiCCutils
- tidybayes
- tidymodels
- Tika
- tiktoken
- TiMBL
- time
- timm
- TINKER
- tiny-cuda-nn
- TinyDB
- TinyXML
- Tk
- Tkinter
- TM-align
- tMAE
- tmap
- tmux
- TN93
- TOBIAS
- ToFu
- Togl
- toil
- tokenizers
- Tombo
- TOML-Fortran
- TOPAS
- topaz
- TopHat
- torch-em
- torchaudio
- torchdata
- torchinfo
- TorchIO
- torchsampler
- torchtext
- torchvf
- torchvision
- tornado
- TotalView
- tox
- tqdm
- Tracer
- TranscriptClean
- TransDecoder
- Transformers
- Transrate
- travis
- TRAVIS-Analyzer
- treatSens
- TreeMix
- TreeShrink
- TRF
- Triangle
- Trilinos
- Trim_Galore
- trimAl
- trimesh
- Trimmomatic
- Trinity
- Trinotate
- Triplexator
- TRIQS
- TRIQS-cthyb
- TRIQS-dft_tools
- TRIQS-tprf
- Triton
- tRNAscan-SE
- TRUST
- TRUST4
- Trycycler
- tseriesEntropy
- tsne
- turbinesFoam
- TurboVNC
- TVB
- tvb-data
- TVB-deps
- tvb-framework
- tvb-library
- TWL-NINJA
- TXR
- typing-extensions
- u
- UCC
- UCC-CUDA
- UCLUST
- UCX
- UCX-CUDA
- ucx-py
- UCX-ROCm
- udocker
- UDUNITS
- UFL
- Ultralytics
- umap-learn
- UMI-tools
- umi4cPackage
- umis
- Umpire
- UNAFold
- uncertainties
- uncertainty-calibration
- Uni-Core
- unicore-uftp
- Unicycler
- Unidecode
- unifdef
- UniFrac
- unimap
- units
- unixODBC
- unrar
- UnZip
- UQTk
- USEARCH
- UShER
- USPEX
- utf8proc
- util-linux
- v
- V8
- vaeda
- Vala
- Valgrind
- Vamb
- Vampir
- Vampire
- VAMPIRE-ASM
- VarDict
- variant_tools
- VariantMetaCaller
- VarScan
- vartools
- VASP
- VAtools
- vawk
- VBZ-Compression
- VCF-kit
- vcflib
- vcfnp
- VCFtools
- vConTACT2
- VEGAS
- velocyto
- Velvet
- VEP
- verifyBamID
- VERSE
- versioningit
- VESTA
- ViennaRNA
- vigra
- Vim
- VirSorter
- VirSorter2
- virtualenv
- VirtualGL
- Virtuoso-opensource
- visdom
- Visit
- vispr
- VisPy
- vitessce-python
- vitessceR
- VMD
- VMTK
- voltools
- vorbis-tools
- Voro++
- vsc-base
- vsc-install
- vsc-mympirun
- vsc-mympirun-scoop
- vsc-processcontrol
- VSCode
- VSEARCH
- vt
- VTK
- VTune
- VV
- VXL
- w
- waLBerla
- wandb
- Wannier90
- WannierTools
- Wayland
- Waylandpp
- WCSLIB
- WCT
- wcwidth
- webin-cli
- WebKitGTK+
- weblogo
- WebSocket++
- WEKA
- WFA2
- wfdb
- WGDgc
- wget
- wgsim
- WHAM
- WhatsHap
- wheel
- WIEN2k
- WildMagic
- Winnowmap
- WisecondorX
- WISExome
- wkhtmltopdf
- worker
- wpebackend-fdo
- WPS
- wradlib
- wrapt
- WRF
- WRF-Fire
- wrf-python
- WSClean
- wtdbg2
- wxPropertyGrid
- wxPython
- wxWidgets
- x
- X11
- x13as
- x264
- x265
- XALT
- xarray
- XBeach
- xbitmaps
- xcb-proto
- xcb-util
- xcb-util-image
- xcb-util-keysyms
- xcb-util-renderutil
- xcb-util-wm
- xCell
- XCFun
- xclip
- XCrySDen
- xdotool
- Xerces-C++
- xESMF
- xextproto
- xf86vidmodeproto
- XGBoost
- XGrafix
- xineramaproto
- XKeyboardConfig
- XlsxWriter
- XMDS2
- Xmipp
- xmitgcm
- XML-Compile
- XML-LibXML
- XML-Parser
- xmlf90
- XMLSec
- XMLStarlet
- xonsh
- XOOPIC
- xorg-macros
- xpdf
- XPLOR-NIH
- xprop
- xproto
- XSD
- xskillscore
- XTandem
- xtb
- xtb-IFF
- xtensor
- xtrans
- Xvfb
- xxd
- xxHash
- XZ
- y
- YACS
- Yade
- yaff
- Yambo
- yaml-cpp
- YANK
- YAPS
- Yasm
- YAXT
- yell
- yelp-tools
- yelp-xsl
- Yices
- YODA
- yt
- z
- Z3
- z5py
- zarr
- Zeo++
- ZeroMQ
- zeus-mcmc
- zfp
- Zgoubi
- ZIMPL
- zingeR
- Zip
- zlib
- zlib-ng
- zlibbioc
- Zoltan
- Zopfli
- ZPAQ
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(quick links: 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/0/","title":"List of supported software (0)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/0/3d-dna/","title":"3d-dna","text":"3D de novo assembly (3D DNA) pipeline
homepage: https://github.com/theaidenlab/3d-dna
version versionsuffix toolchain 180922 -Python-2.7.15 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/0/3to2/","title":"3to2","text":"lib3to2 is a set of fixers that are intended to backport code written for Python version 3.x into Python version 2.x.
homepage: https://pypi.python.org/pypi/3to2
version versionsuffix toolchain 1.1.1 -Python-2.7.12 foss/2016b 1.1.1 -Python-2.7.12 intel/2016b 1.1.1 -Python-2.7.13 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/0/4ti2/","title":"4ti2","text":"A software package for algebraic, geometric and combinatorial problems on linear spaces
homepage: https://4ti2.github.io/
version toolchain 1.6.10 GCC/13.2.0 1.6.9 GCC/11.3.0 1.6.9 GCC/8.2.0-2.31.1 1.6.9 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/","title":"List of supported software (a)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- ABAQUS
- ABINIT
- ABRA2
- ABRicate
- Abseil
- absl-py
- abTEM
- ABySS
- accelerate
- ack
- ACTC
- ada
- AdapterRemoval
- ADDA
- ADF
- ADIOS
- adjustText
- ADMIXTURE
- ADOL-C
- Advisor
- AEDT
- affinity
- affogato
- AFNI
- AGAT
- AGeNT
- AGFusion
- AICSImageIO
- AIMAll
- aiohttp
- ALADIN
- ALAMODE
- Albacore
- Albumentations
- alevin-fry
- ALFA
- Alfred
- ALL
- alleleCount
- alleleIntegrator
- Allinea
- ALLPATHS-LG
- almosthere
- Alpha
- AlphaFold
- AlphaPulldown
- ALPS
- alsa-lib
- AMAPVox
- Amara
- amask
- Amber
- AmberMini
- AmberTools
- AMD-LibM
- AMD-RNG
- AMD-SecureRNG
- AMD-uProf
- amdahl
- AMGX
- AMICA
- AMOS
- AMPHORA2
- AMPL-MP
- amplimap
- AMPtk
- AMRFinderPlus
- AmrPlusPlus
- AMS
- Anaconda2
- Anaconda3
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- aNCI
- andi
- ANGEL
- angsd
- ANIcalculator
- anndata
- Annif
- Annocript
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- ant
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- antiSMASH
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- anvio
- any2fasta
- AOCC
- AOFlagger
- AOMP
- APBS
- apex
- APOST3D
- APR
- APR-util
- AptaSUITE
- ARAGORN
- Arb
- Arcade-Learning-Environment
- arcasHLA
- ARCH
- Archive-Zip
- ArchR
- archspec
- AreTomo2
- ARGoS
- argtable
- aria2
- Arlequin
- Armadillo
- arosics
- ARPACK++
- arpack-ng
- ArrayFire
- Arriba
- Arrow
- arrow-R
- ART
- Artemis
- artic-ncov2019
- ARTS
- ArviZ
- ARWEN
- ASAP
- ASAP3
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- ASF-SearchAPI
- ASHS
- Aspera-CLI
- Aspera-Connect
- assembly-stats
- assimp
- Assimulo
- ASTRID
- astro-tulips
- astropy
- at-spi2-atk
- at-spi2-core
- ATAT
- ATK
- ATLAS
- atomate
- AtomPAW
- atools
- atropos
- ATSAS
- attr
- attrdict
- attrdict3
- augur
- AUGUSTUS
- Austin
- AUTO-07p
- Autoconf
- Autoconf-archive
- AutoDock
- AutoDock-GPU
- AutoDock-Vina
- AutoDockSuite
- AutoGeneS
- AutoGrid
- Automake
- AutoMap
- autopep8
- Autotools
- Avogadro2
- avro-cpp
- awscli
- Ax
- axel
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ABAQUS/","title":"ABAQUS","text":"Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.
homepage: http://www.simulia.com/products/abaqus_fea.html
version versionsuffix toolchain 2017 -hotfix-1721 system 2018 -hotfix-1806 system 2020 system 2021 -hotfix-2132 system 2022 -hotfix-2214 system 2022 -hotfix-2223 system 2022 system 6.12.1 -linux-x86_64 system 6.13.5 -linux-x86_64 system 6.14.1 -linux-x86_64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ABINIT/","title":"ABINIT","text":"Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.
homepage: http://www.abinit.org/
version versionsuffix toolchain 7.0.3 -x86_64_linux_gnu4.5 system 7.0.5 -x86_64_linux_gnu4.5 system 7.10.5 -libxc intel/2016.02-GCC-4.9 7.10.5 intel/2016.02-GCC-4.9 7.2.1 -x86_64_linux_gnu4.5 system 8.0.8 intel/2016a 8.0.8b foss/2016b 8.0.8b intel/2016b 8.10.2 intel/2018b 8.10.3 intel/2018b 8.2.2 foss/2016b 8.2.2 intel/2016b 8.4.4 intel/2017b 8.6.3 intel/2018a 9.10.3 intel/2022a 9.2.1 foss/2019b 9.2.1 intel/2019b 9.2.1 intel/2020a 9.4.1 foss/2020b 9.4.1 intel/2020a 9.4.1 intel/2020b 9.4.2 foss/2021a 9.4.2 intel/2021a 9.6.2 foss/2022a 9.6.2 intel/2021a 9.6.2 intel/2021b 9.6.2 intel/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ABRA2/","title":"ABRA2","text":"Assembly Based ReAligner
homepage: https://github.com/mozack/abra2
version toolchain 2.22 iccifort/2019.5.281 2.23 GCC/10.2.0 2.23 GCC/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ABRicate/","title":"ABRicate","text":"Mass screening of contigs for antimicrobial and virulence genes
homepage: https://github.com/tseemann/abricate
version versionsuffix toolchain 0.9.9 -Perl-5.28.1 gompi/2019a 0.9.9 gompi/2019b 1.0.0 gompi/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ABySS/","title":"ABySS","text":"Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss
version toolchain 1.9.0 foss/2016a 2.0.2 foss/2016b 2.0.2 foss/2018a 2.0.2 gompi/2019a 2.0.2 intel/2016b 2.0.3 foss/2017b 2.0.3 intel/2017b 2.1.5 foss/2019b 2.2.5 foss/2020b 2.3.7 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ACTC/","title":"ACTC","text":"ACTC converts independent triangles into triangle strips or fans.
homepage: https://sourceforge.net/projects/actc
version toolchain 1.1 GCCcore/10.2.0 1.1 GCCcore/11.3.0 1.1 GCCcore/6.4.0 1.1 GCCcore/7.3.0 1.1 GCCcore/8.3.0 1.1 GCCcore/9.3.0 1.1 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ADDA/","title":"ADDA","text":"ADDA is an open-source parallel implementation of the discrete dipole approximation, capable to simulate light scattering by particles of arbitrary shape and composition in a wide range of particle sizes.
homepage: https://github.com/adda-team/adda/wiki
version toolchain 1.3b4 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ADF/","title":"ADF","text":"ADF is a premium-quality quantum chemistry software package based on Density Functional Theory (DFT).
homepage: http://www.scm.com/
version versionsuffix toolchain 2009.01a.pc64_linux.intelmpi system 2014.02 system 2014.11.r48287 intel/2016a 2016.101 system 2019.303 -intelmpi system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ADIOS/","title":"ADIOS","text":"The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation.
homepage: https://www.olcf.ornl.gov/center-projects/adios/
version versionsuffix toolchain 1.13.1 -Python-2.7.15 foss/2019a 1.13.1 -Python-3.8.2 foss/2020a 20210804 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ADMIXTURE/","title":"ADMIXTURE","text":"ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.
homepage: https://dalexander.github.io/admixture/
version toolchain 1.3.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ADOL-C/","title":"ADOL-C","text":"The package ADOL-C (Automatic Differentiation by OverLoading in C++) facilitates the evaluation of first and higher derivatives of vector functions that are defined by computer programs written in C or C++. The resulting derivative evaluation routines may be called from C/C++, Fortran, or any other language that can be linked with C.
homepage: https://projects.coin-or.org/ADOL-C
version toolchain 2.7.0 gompi/2019a 2.7.2 gompi/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AEDT/","title":"AEDT","text":"The Ansys Electronics Desktop (AEDT) is a platform that enables true electronics system design. AEDT provides access to the Ansys gold-standard electromagnetics simulation solutions such as Ansys HFSS, Ansys Maxwell, Ansys Q3D Extractor, Ansys SIwave, and Ansys Icepak using electrical CAD (ECAD) and mechanical CAD (MCAD) workflows.
homepage: https://www.ansys.com/products/electronics
version toolchain 2024R1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AFNI/","title":"AFNI","text":"AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.
homepage: http://afni.nimh.nih.gov/
version versionsuffix toolchain 18.1.09 -Python-3.6.4 intel/2018a 18.3.00 -Python-3.6.6 foss/2018b 19.0.01 -Python-2.7.14 foss/2017b 19.0.01 -Python-2.7.14 intel/2017b 20160329 -Python-2.7.11 intel/2016a 24.0.02 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AGAT/","title":"AGAT","text":"AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format.
homepage: https://agat.readthedocs.io/en/latest/
version toolchain 0.9.2 GCC/11.2.0 1.1.0 GCC/12.2.0 1.4.0 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AGFusion/","title":"AGFusion","text":"AGFusion is a python package for annotating gene fusions from the human or mouse genomes.
homepage: https://github.com/murphycj/AGFusion
version versionsuffix toolchain 1.2 -Python-3.7.2 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AGeNT/","title":"AGeNT","text":"The Agilent Genomics NextGen Toolkit (AGeNT) is a Java-based software module that processes the read sequences from targeted high-throughput sequencing data generated by sequencing Agilent SureSelect and HaloPlex libraries. The Trimmer utility of the AGeNT module processes the read sequences to identify and remove the adaptor sequences and extracts dual molecular barcodes (for SureSelect XT HS2). The LocatIt utility of the AGeNT module processes the Molecular Barcode (MBC) information from HaloPlex HS, SureSelect XT HS, and SureSelect XT HS2 Illumina sequencing runs with options to either mark or merge duplicate reads and output in BAM file format. The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files produced by Illumina sequencers including NextSeq 1k/2k. These libraries are backwards compatible and capable of supporting prior releases of the software, with one exception: GA systems have been excluded.
homepage: https://www.agilent.com/en/product/next-generation-sequencing/hybridization-based-next-generation-sequencing-ngs/ngs-software/agent-232879
version toolchain 3.0.6 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AICSImageIO/","title":"AICSImageIO","text":"Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python
homepage: https://github.com/AllenCellModeling/aicsimageio
version toolchain 4.14.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AIMAll/","title":"AIMAll","text":"AIMAll is an easy to use, accurate, reliable and efficient quantum chemistry software package for performing comprehensive, quantitative and visual QTAIM analyses of molecular systems - starting from molecular wavefunction data.
homepage: http://aim.tkgristmill.com
version versionsuffix toolchain 19.10.12 -linux_64bit intel/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ALADIN/","title":"ALADIN","text":"ALADIN was entirely built on the notion of compatibility with its mother system, IFS/ARPEG. The latter, a joint development between the European Centre for Medium-Range Weather Forecasts (ECMWF) and Meteo-France, was only meant to consider global Numerical Weather Prediction applications; hence the idea, for ALADIN, to complement the IFS/ARPEGE project with a limited area model (LAM) version, while keeping the differences between the two softwares as small as possible.
homepage: http://www.cnrm.meteo.fr/aladin/
version toolchain 36t1_op2bf1 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ALAMODE/","title":"ALAMODE","text":"ALAMODE is an open source software designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles.
homepage: http://alamode.readthedocs.io/en/latest/index.html
version toolchain 1.4.2 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ALFA/","title":"ALFA","text":"ALFA provides a global overview of features distribution composing NGS dataset(s). Given a set of aligned reads (BAM files) and an annotation file (GTF format), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, 5'-UTR, CDS, intergenic, etc.) and biotypes (protein coding genes, miRNA, tRNA, etc.). Whatever the sequencing technique, whatever the organism.
homepage: https://github.com/biocompibens/ALFA
version versionsuffix toolchain 1.1.1 -Python-3.7.2 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ALL/","title":"ALL","text":"A Load Balancing Library (ALL) aims to provide an easy way to include dynamic domain-based load balancing into particle based simulation codes. The library is developed in the Simulation Laboratory Molecular Systems of the J\u00fclich Supercomputing Centre at Forschungszentrum J\u00fclich.
homepage: https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing
version toolchain 0.9.2 foss/2022b 0.9.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ALLPATHS-LG/","title":"ALLPATHS-LG","text":"ALLPATHS-LG, the new short read genome assembler.
homepage: http://www.broadinstitute.org/software/allpaths-lg/blog/
version toolchain 52488 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ALPS/","title":"ALPS","text":"The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as C++ libraries for simplifying the development of such code.
homepage: http://www.example.com
version versionsuffix toolchain 2.2.b4 -Python-2.7.11 intel/2016a 2.3.0 -Python-2.7.12 foss/2016b 2.3.0 -Python-3.5.2 foss/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AMAPVox/","title":"AMAPVox","text":"LiDAR data voxelisation software
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version versionsuffix toolchain 1.9.4 -Java-11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AMD-LibM/","title":"AMD-LibM","text":"AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor based machines.
homepage: https://developer.amd.com/amd-cpu-libraries/amd-math-library-libm/
version toolchain 3.2.2 GCC/7.3.0-2.30 3.6.0-4 GCC/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AMD-RNG/","title":"AMD-RNG","text":"AMD Random Number Generator Library is a pseudorandom number generator library.
homepage: https://developer.amd.com/amd-cpu-libraries/rng-library/
version toolchain 1.0 GCC/7.3.0-2.30 2.2-4 GCC/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AMD-SecureRNG/","title":"AMD-SecureRNG","text":"The AMD Secure Random Number Generator (RNG) is a library that provides APIs to access the cryptographically secure random numbers generated by AMD\u2019s hardware-based random number generator implementation.
homepage: https://developer.amd.com/amd-cpu-libraries/rng-library/
version toolchain 1.0 GCC/7.3.0-2.30 2.2-4 GCC/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AMD-uProf/","title":"AMD-uProf","text":"AMD uProf is a performance analysis tool for applications running on Windows, Linux & FreeBSD operating systems. It allows developers to better understand the runtime performance of their application and to identify ways to improve its performance.
homepage: https://developer.amd.com/amd-uprof/
version toolchain 3.4.502 system 3.5.671 system 4.1.424 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AMGX/","title":"AMGX","text":"Distributed multigrid linear solver library on GPU
homepage: https://github.com/NVIDIA/AMGX
version versionsuffix toolchain 2.4.0 -CUDA-12.1.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AMICA/","title":"AMICA","text":"Code for AMICA: Adaptive Mixture ICA with shared components
homepage: https://github.com/sccn/amica
version toolchain 2024.1.19 intel/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AMOS/","title":"AMOS","text":"The AMOS consortium is committed to the development of open-source whole genome assembly software
homepage: http://amos.sourceforge.net
version toolchain 3.1.0 foss/2018b 3.1.0 foss/2021b 3.1.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AMPHORA2/","title":"AMPHORA2","text":"An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
homepage: https://github.com/wu-lab-uva/AMPHORA2
version versionsuffix toolchain 20190730 -Java-13-pthreads-avx2 gompi/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AMPL-MP/","title":"AMPL-MP","text":"An open-source library for mathematical programming.
homepage: https://github.com/ampl/mp
version toolchain 3.1.0 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AMPtk/","title":"AMPtk","text":"AMPtk is a series of scripts to process NGS amplicon data using USEARCH and VSEARCH, it can also be used to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial 16S, and insect COI amplicons.
homepage: https://amptk.readthedocs.io
version toolchain 1.5.4 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AMRFinderPlus/","title":"AMRFinderPlus","text":"This software and the accompanying database are designed to find acquired antimicrobial resistance genes and some point mutations in protein or assembled nucleotide sequences.
homepage: https://github.com/ncbi/amr
version toolchain 3.11.18 gompi/2021b 3.11.18 gompi/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AMS/","title":"AMS","text":"The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for computational chemistry and materials science, from quantum mechanics to fluid thermodynamics.
homepage: https://www.scm.com/amsterdam-modeling-suite/
version versionsuffix toolchain 2020.102 -intelmpi iimpi/2020b 2022.102 -intelmpi iimpi/2021b 2023.101 -intelmpi iimpi/2022a 2023.104 -intelmpi iimpi/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ANGEL/","title":"ANGEL","text":"ANGEL: Robust Open Reading Frame prediction
homepage: https://github.com/PacificBiosciences/ANGEL
version versionsuffix toolchain 3.0 -Python-3.7.2 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ANIcalculator/","title":"ANIcalculator","text":"This tool will calculate the bidirectional average nucleotide identity (gANI) and Alignment Fraction (AF) between two genomes. Required input is the full path to the fna file (nucleotide sequence of genes in fasta format) of each query genome. Either the rRNA and tRNA genes can be excluded, or provided in a list with the -ignoreList option. This is necessary as the presence of tRNA and/or rRNA genes in the fna will artificially inflate the ANI.
homepage: https://ani.jgi.doe.gov/html/home.php
version toolchain 1.0 GCCcore/10.3.0 1.0 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ANSYS/","title":"ANSYS","text":"ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater.
homepage: http://www.ansys.com
version toolchain 15.0 system 2022R2 system 2023R1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ANSYS_CFD/","title":"ANSYS_CFD","text":"ANSYS computational fluid dynamics (CFD) simulation software allows you to predict, with confidence, the impact of fluid flows on your product throughout design and manufacturing as well as during end use. ANSYS renowned CFD analysis tools include the widely used and well-validated ANSYS Fluent and ANSYS CFX.
homepage: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics
version toolchain 16.2 system 17.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ANTIC/","title":"ANTIC","text":"Antic is an algebraic number theory library.
homepage: https://github.com/flintlib/antic
version toolchain 0.2.5 gfbf/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ANTLR/","title":"ANTLR","text":"ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions.
homepage: https://www.antlr2.org/
version versionsuffix toolchain 2.7.7 -Java-11 GCCcore/10.2.0 2.7.7 -Java-11 GCCcore/10.3.0 2.7.7 -Java-11 GCCcore/11.2.0 2.7.7 -Java-11 GCCcore/11.3.0 2.7.7 -Java-11 GCCcore/12.3.0 2.7.7 GCCcore/7.3.0 2.7.7 GCCcore/8.2.0 2.7.7 -Java-11 GCCcore/8.3.0 2.7.7 -Java-11 GCCcore/9.3.0 2.7.7 -Python-2.7.11 foss/2016a 2.7.7 foss/2017b 2.7.7 -Python-2.7.14 foss/2018a 2.7.7 foss/2018b 2.7.7 foss/2019a 2.7.7 -Python-2.7.13 intel/2017a 2.7.7 -Python-2.7.14 intel/2017b 2.7.7 intel/2017b 2.7.7 -Python-3.6.4 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ANTs/","title":"ANTs","text":"ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.
homepage: http://stnava.github.io/ANTs/
version versionsuffix toolchain 2.2.0 -Python-2.7.12 foss/2016b 2.3.0 -Python-2.7.14 foss/2017b 2.3.0 -Python-2.7.14 intel/2017b 2.3.1 -Python-3.6.6 foss/2018b 2.3.2 -Python-3.7.4 foss/2019b 2.3.5 foss/2021a 2.5.0 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AOCC/","title":"AOCC","text":"AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 11.0
homepage: https://developer.amd.com/amd-aocc/
version toolchain 2.3.0 GCCcore/10.2.0 2.3.0 GCCcore/9.3.0 3.0.0 GCCcore/10.2.0 3.0.0 GCCcore/10.3.0 3.1.0 GCCcore/10.2.0 3.1.0 GCCcore/10.3.0 3.1.0 GCCcore/11.2.0 3.2.0 GCCcore/11.2.0 3.2.0 GCCcore/11.3.0 4.0.0 GCCcore/11.3.0 4.0.0 GCCcore/12.2.0 4.0.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AOFlagger/","title":"AOFlagger","text":"The AOFlagger is a tool that can find and remove radio-frequency interference (RFI) in radio astronomical observations. It can make use of Lua scripts to make flagging strategies flexible, and the tools are applicable to a wide set of telescopes.
homepage: https://aoflagger.readthedocs.io/
version toolchain 3.4.0 foss/2022a 3.4.0 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AOMP/","title":"AOMP","text":"AMD fork of LLVM, setup for OpenMP offloading to Accelerators
homepage: https://github.com/ROCm-Developer-Tools/aomp
version toolchain 13.0-2 GCCcore/10.2.0 13.0-2 gcccuda/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/APBS/","title":"APBS","text":"APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media.
homepage: http://www.poissonboltzmann.org/apbs
version versionsuffix toolchain 1.4 -linux-static-x86_64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/APOST3D/","title":"APOST3D","text":"Open-source APOST-3D software features a large number of wavefunction analysis tools developed over the past 20 years, aiming at connecting classical chemical concepts with the electronic structure of molecules. APOST-3D relies on the identification of the atom in the molecule (AIM), and several analysis tools are implemented in the most general way so that they can be used in combination with any chosen AIM. A Fortran-based code developed at the Universitat de Girona (UdG) by P. Salvador and collaborators.
homepage: https://github.com/mgimferrer/APOST3D
version toolchain 20240527 intel-compilers/2023.1.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/APR-util/","title":"APR-util","text":"Apache Portable Runtime (APR) util libraries.
homepage: https://apr.apache.org/
version toolchain 1.6.1 GCCcore/10.2.0 1.6.1 GCCcore/10.3.0 1.6.1 GCCcore/11.2.0 1.6.1 GCCcore/11.3.0 1.6.1 GCCcore/6.4.0 1.6.1 GCCcore/7.3.0 1.6.1 GCCcore/8.2.0 1.6.1 GCCcore/9.3.0 1.6.1 iomkl/2018a 1.6.3 GCCcore/12.3.0 1.6.3 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/APR/","title":"APR","text":"Apache Portable Runtime (APR) libraries.
homepage: http://apr.apache.org/
version toolchain 1.6.3 GCCcore/6.4.0 1.6.3 GCCcore/7.3.0 1.6.3 iomkl/2018a 1.7.0 GCCcore/10.2.0 1.7.0 GCCcore/10.3.0 1.7.0 GCCcore/11.2.0 1.7.0 GCCcore/11.3.0 1.7.0 GCCcore/8.2.0 1.7.0 GCCcore/9.3.0 1.7.4 GCCcore/12.3.0 1.7.4 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ARAGORN/","title":"ARAGORN","text":"a program to detect tRNA genes and tmRNA genes in nucleotide sequences
homepage: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
version toolchain 1.2.38 foss/2016b 1.2.38 iccifort/2019.5.281 1.2.41 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ARCH/","title":"ARCH","text":"Autoregressive Conditional Heteroskedasticity (ARCH) and other tools for financial econometrics, written in Python (with Cython and/or Numba used to improve performance).
homepage: https://pypi.org/project/arch
version versionsuffix toolchain 4.5.0 -Python-3.6.4 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ARGoS/","title":"ARGoS","text":"A parallel, multi-engine simulator for heterogeneous swarm robotics
homepage: http://www.argos-sim.info
version versionsuffix toolchain 3.0.0-beta53 -Lua-5.2.4 foss/2018b 3.0.0-beta59 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ARPACK%2B%2B/","title":"ARPACK++","text":"Arpackpp is a C++ interface to the ARPACK Fortran package, which implements the implicit restarted Arnoldi method for iteratively solving large-scale sparse eigenvalue problems.
homepage: https://github.com/m-reuter/arpackpp
version toolchain 2018.03.26 foss/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ART/","title":"ART","text":"ART is a set of simulation tools to generate synthetic next-generation sequencing reads\"
homepage: http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
version toolchain 2016.06.05 GCCcore/6.4.0 2016.06.05 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ARTS/","title":"ARTS","text":"ARTS is a radiative transfer model for the millimeter and sub-millimeter spectral range. There are a number of models mostly developed explicitly for the different sensors.
homepage: http://www.radiativetransfer.org/
version toolchain 2.2.64 gompi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ARWEN/","title":"ARWEN","text":"ARWEN, tRNA detection in metazoan mitochondrial sequences
homepage: http://mbio-serv2.mbioekol.lu.se/ARWEN
version toolchain 1.2.3 GCCcore/7.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ASAP/","title":"ASAP","text":"ASAP focuses on fast and fluid image viewing with an easy-to-use interface for making annotations. It consists of two main components: an IO library for reading and writing multi-resolution images and a viewer component for visualizing such images.
homepage: https://computationalpathologygroup.github.io/ASAP/
version versionsuffix toolchain 2.0 -CUDA-11.3.1 foss/2021a 2.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ASAP3/","title":"ASAP3","text":"ASAP is a calculator for doing large-scale classical molecular dynamics within the Campos Atomic Simulation Environment (ASE).
homepage: https://wiki.fysik.dtu.dk/asap/
version versionsuffix toolchain 3.10.10 -Python-3.6.6 foss/2018b 3.10.10 -Python-3.6.6 intel/2018b 3.10.10 -Python-3.6.6 iomkl/2018b 3.10.7 -Python-3.5.2 foss/2016b 3.10.7 -Python-3.6.2 foss/2017b 3.10.8 -Python-3.5.2 foss/2016b 3.10.8 -Python-3.6.2 foss/2017b 3.10.8 -Python-3.6.3 foss/2017b 3.11.10 -Python-3.7.2 foss/2019a 3.11.10 -Python-3.7.2 intel/2019a 3.12.2 -ASE-3.21.1 foss/2020b 3.12.2 -ASE-3.21.1 intel/2020b 3.12.7 -ASE-3.21.1 foss/2020b 3.12.7 -ASE-3.21.1 intel/2020b 3.13.2 foss/2023a 3.13.3 foss/2023a 3.13.3 intel/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ASCAT/","title":"ASCAT","text":"ASCAT is a method to derive copy number profiles of tumor cells, accounting for normal cell admixture and tumor aneuploidy.
homepage: https://github.com/VanLoo-lab/ascat
version versionsuffix toolchain 3.1.2 -R-4.2.1 foss/2022a 3.1.2 -R-4.2.2 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ASE/","title":"ASE","text":"ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.
homepage: http://wiki.fysik.dtu.dk/ase
version versionsuffix toolchain 3.10.0 -Python-2.7.11 intel/2016.02-GCC-4.9 3.11.0 -Python-2.7.12 intel/2016b 3.13.0 -Python-2.7.12 foss/2016b 3.13.0 -Python-2.7.13 intel/2017a 3.15.0 -Python-2.7.12 foss/2016b 3.15.0 -Python-3.5.2 foss/2016b 3.15.0 -Python-3.6.2 foss/2017b 3.15.0 -Python-3.6.3 foss/2017b 3.15.0 -Python-2.7.14 intel/2017b 3.16.2 -Python-3.6.6 foss/2018b 3.16.2 -Python-3.6.6 intel/2018b 3.16.2 -Python-3.6.4 iomkl/2018.02 3.16.2 -Python-3.6.4 iomkl/2018a 3.16.2 -Python-3.6.6 iomkl/2018b 3.17.0 -Python-3.6.6 foss/2018b 3.17.0 -Python-3.7.2 foss/2019a 3.17.0 -Python-3.6.6 intel/2018b 3.17.0 -Python-3.7.2 intel/2019a 3.17.0 -Python-3.6.6 iomkl/2018b 3.18.0 -Python-3.6.6 foss/2018b 3.18.0 -Python-3.7.2 foss/2019a 3.18.0 -Python-3.6.6 intel/2018b 3.18.0 -Python-3.7.2 intel/2019a 3.19.0 -Python-3.6.6 foss/2018b 3.19.0 -Python-3.7.4 foss/2019b 3.19.0 -Python-3.8.2 foss/2020a 3.19.0 -Python-3.7.4 fosscuda/2019b 3.19.0 -Python-3.6.6 intel/2018b 3.19.0 -Python-3.7.4 intel/2019b 3.19.0 -Python-3.8.2 intel/2020a 3.20.1 -Python-3.7.4 foss/2019b 3.20.1 foss/2020b 3.20.1 fosscuda/2020b 3.20.1 -Python-3.7.4 intel/2019b 3.20.1 -Python-3.8.2 intel/2020a 3.20.1 intel/2020b 3.21.1 -Python-3.8.2 foss/2020a 3.21.1 foss/2020b 3.21.1 fosscuda/2020b 3.21.1 intel/2020b 3.22.0 foss/2020b 3.22.0 foss/2021a 3.22.0 fosscuda/2020b 3.22.0 intel/2020b 3.22.0 intel/2021a 3.22.1 foss/2021b 3.22.1 foss/2022a 3.22.1 gfbf/2022b 3.22.1 gfbf/2023a 3.22.1 gomkl/2021a 3.22.1 iimkl/2023a 3.22.1 intel/2021b 3.22.1 intel/2022a 3.23.0 gfbf/2023a 3.23.0 iimkl/2023a 3.9.1.4567 -Python-2.7.11 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ASF-SearchAPI/","title":"ASF-SearchAPI","text":"asf_search is a Python module for performing searches of the ASF catalog. In addition, it offers baseline functionality and download support.
homepage: https://docs.asf.alaska.edu/
version toolchain 6.5.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ASHS/","title":"ASHS","text":"Automatic Segmentation of Hippocampal Subfields (ASHS)
homepage: https://sites.google.com/site/hipposubfields/home
version toolchain rev103_20140612 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ASTRID/","title":"ASTRID","text":"ASTRID-2 is a method for estimating species trees from gene trees.
homepage: https://github.com/pranjalv123/ASTRID
version toolchain 2.2.1 gompi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ATAT/","title":"ATAT","text":"The Alloy-Theoretic Automated Toolkit (ATAT) is a generic name that refers to a collection of alloy theory tools
homepage: https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/
version toolchain 3.36 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/ATK/","title":"ATK","text":"ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.
homepage: https://developer.gnome.org/ATK/stable/
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","boost":0.5},{"location":"version-specific/supported-software/a/ATLAS/","title":"ATLAS","text":"ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library.
homepage: http://math-atlas.sourceforge.net
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","boost":0.5},{"location":"version-specific/supported-software/a/ATSAS/","title":"ATSAS","text":"ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules.
homepage: http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html
version versionsuffix toolchain 2.5.1-1 .el6.x86_64 system 2.5.1-1 .sl5.x86_64 system 2.7.1-1 .el7.x86_64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AUGUSTUS/","title":"AUGUSTUS","text":"AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
homepage: http://bioinf.uni-greifswald.de/augustus/
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","boost":0.5},{"location":"version-specific/supported-software/a/AUTO-07p/","title":"AUTO-07p","text":"AUTO is a publicly available software for continuation and bifurcation problems in ordinary differential equations originally written in 1980 and widely used in the dynamical systems community.
homepage: https://github.com/auto-07p
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","boost":0.5},{"location":"version-specific/supported-software/a/Abseil/","title":"Abseil","text":"Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google's own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives.
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","boost":0.5},{"location":"version-specific/supported-software/a/AdapterRemoval/","title":"AdapterRemoval","text":"AdapterRemoval searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal.
homepage: https://github.com/MikkelSchubert/adapterremoval
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","boost":0.5},{"location":"version-specific/supported-software/a/Advisor/","title":"Advisor","text":"Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance \u201cdies\u201d - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain
homepage: https://software.intel.com/intel-advisor-xe
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","boost":0.5},{"location":"version-specific/supported-software/a/Albacore/","title":"Albacore","text":"Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms.
homepage: https://community.nanoporetech.com/protocols/albacore-offline-basecalli/v/abec_2003_v1_revz_29nov2016
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","boost":0.5},{"location":"version-specific/supported-software/a/Albumentations/","title":"Albumentations","text":"Albumentations is a Python library for fast and flexible image augmentations
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","boost":0.5},{"location":"version-specific/supported-software/a/Alfred/","title":"Alfred","text":"Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner. Alfred supports read counting, feature annotation and haplotype-resolved consensus computation using multiple sequence alignments.
homepage: https://www.gear-genomics.com/alfred/
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","boost":0.5},{"location":"version-specific/supported-software/a/Allinea/","title":"Allinea","text":"The Allinea environment is an essential toolkit for developers and computational scientists looking to get results faster.
homepage: http://www.allinea.com
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","boost":0.5},{"location":"version-specific/supported-software/a/Alpha/","title":"Alpha","text":"Alpha is a tool designed for detailed comparative study of bacteriophage genomes.
homepage: https://www.lirmm.fr/~swenson/alpha/alpha.htm
version versionsuffix toolchain 20200430 -Python-2.7.16 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/AlphaFold/","title":"AlphaFold","text":"AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known
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","boost":0.5},{"location":"version-specific/supported-software/a/AlphaPulldown/","title":"AlphaPulldown","text":"AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer
homepage: https://github.com/KosinskiLab/AlphaPulldown
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","boost":0.5},{"location":"version-specific/supported-software/a/Amara/","title":"Amara","text":"Library for XML processing in Python, designed to balance the native idioms of Python with the native character of XML.
homepage: https://pypi.org/project/Amara
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","boost":0.5},{"location":"version-specific/supported-software/a/Amber/","title":"Amber","text":"Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.
homepage: http://ambermd.org/amber.html
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","boost":0.5},{"location":"version-specific/supported-software/a/AmberMini/","title":"AmberMini","text":"A stripped-down set of just antechamber, sqm, and tleap.
homepage: https://github.com/choderalab/ambermini
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","boost":0.5},{"location":"version-specific/supported-software/a/AmberTools/","title":"AmberTools","text":"AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.
homepage: https://ambermd.org/
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","boost":0.5},{"location":"version-specific/supported-software/a/AmrPlusPlus/","title":"AmrPlusPlus","text":"AmrPlusPlus v2.0 can process the raw data from the sequencer, identify the fragments of DNA, and count them. It also provides a count of the polymorphisms that occur in each DNA fragment with respect to the reference database.
homepage: https://megares.meglab.org/amrplusplus/latest/html/v2
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","boost":0.5},{"location":"version-specific/supported-software/a/Anaconda2/","title":"Anaconda2","text":"Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
homepage: https://www.anaconda.com
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","boost":0.5},{"location":"version-specific/supported-software/a/Anaconda3/","title":"Anaconda3","text":"Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
homepage: https://www.anaconda.com
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","boost":0.5},{"location":"version-specific/supported-software/a/Annif/","title":"Annif","text":"Annif is a multi-algorithm automated subject indexing tool for libraries, archives and museums.
homepage: https://github.com/NatLibFi/Annif
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","boost":0.5},{"location":"version-specific/supported-software/a/Annocript/","title":"Annocript","text":"Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes blast analysis with UniProt, NCBI Conserved Domain Database and Nucleotide division adding also annotations from Gene Ontology, the Enzyme Commission and UniPathways. Annocript also gives information about the longest ORF and the non-coding potential using external software. Annocript is also capable to identify putative long non-coding RNAs by using an heuristic based on homology and sequence features.
homepage: https://github.com/frankMusacchia/Annocript
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","boost":0.5},{"location":"version-specific/supported-software/a/AptaSUITE/","title":"AptaSUITE","text":"A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments
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","boost":0.5},{"location":"version-specific/supported-software/a/Arb/","title":"Arb","text":"Arb is a C library for arbitrary-precision interval arithmetic. It has full support for both real and complex numbers. The library is thread-safe, portable, and extensively tested.
homepage: http://arblib.org
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homepage: https://github.com/mgbellemare/Arcade-Learning-Environment
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","boost":0.5},{"location":"version-specific/supported-software/a/ArchR/","title":"ArchR","text":"ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data.
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","boost":0.5},{"location":"version-specific/supported-software/a/Archive-Zip/","title":"Archive-Zip","text":"Provide an interface to ZIP archive files.
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","boost":0.5},{"location":"version-specific/supported-software/a/AreTomo2/","title":"AreTomo2","text":"AreTomo2, a multi-GPU accelerated software package that fully automates motion- corrected marker-free tomographic alignment and reconstruction, now includes robust GPU-accelerated CTF (Contrast Transfer Function) estimation in a single package. AreTomo2 is part of our endeavor to build a fully-automated high- throughput processing pipeline that enables real-time reconstruction of tomograms in parallel with tomographic data collection. It strives to be fast and accurate, as well as provides for easy integration into subtomogram processing workflows by generating IMod compatible files containing alignment and CTF parameters needed to bootstrap subtomogram averaging. AreTomo2 can also be used for on-the-fly reconstruction of tomograms and CTF estimation in parallel with tilt series collection, enabling real-time assessment of sample quality and adjustment of collection parameters
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","boost":0.5},{"location":"version-specific/supported-software/a/Arlequin/","title":"Arlequin","text":"Arlequin: An Integrated Software for Population Genetics Data Analysis
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","boost":0.5},{"location":"version-specific/supported-software/a/Armadillo/","title":"Armadillo","text":"Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.
homepage: http://arma.sourceforge.net/
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","boost":0.5},{"location":"version-specific/supported-software/a/ArrayFire/","title":"ArrayFire","text":"ArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices.
homepage: https://arrayfire.com/
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homepage: https://github.com/assimp/assimp
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homepage: https://github.com/hhatto/autopep8
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","boost":0.5},{"location":"version-specific/supported-software/a/avro-cpp/","title":"avro-cpp","text":"C++ implementation of Avro data serialization system.
homepage: https://avro.apache.org
version toolchain 1.11.1 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/awscli/","title":"awscli","text":"Universal Command Line Environment for AWS
homepage: https://pypi.python.org/pypi/awscli
version versionsuffix toolchain 1.11.1 -Python-2.7.12 intel/2016b 1.11.56 -Python-2.7.12 foss/2016b 1.16.290 -Python-3.6.6 foss/2018b 1.17.7 -Python-3.7.4 GCCcore/8.3.0 1.18.89 -Python-3.8.2 GCCcore/9.3.0 2.0.55 -Python-3.8.2 GCCcore/9.3.0 2.11.21 GCCcore/11.3.0 2.15.2 GCCcore/12.2.0 2.17.54 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/a/axel/","title":"axel","text":"Lightweight CLI download accelerator
homepage: https://github.com/axel-download-accelerator/axel
version toolchain 2.17.9 GCCcore/8.3.0 2.17.9 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/","title":"List of supported software (b)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- BA3-SNPS-autotune
- BabelStream
- babl
- Bader
- BAGEL
- BAli-Phy
- bam-readcount
- Bambi
- bamFilters
- BAMM
- BAMSurgeon
- bamtofastq
- BamTools
- BamUtil
- Bandage
- barrnap
- basemap
- bases2fastq
- Bash
- bashplotlib
- bat
- batchgenerators
- BatMeth2
- BayesAss
- BayesAss3-SNPs
- BayeScan
- BayeScEnv
- bayesian-optimization
- BayesOpt
- BayesPrism
- BayesTraits
- Bazel
- bbcp
- bbFTP
- BBMap
- bc
- BCALM
- bcbio-gff
- BCEL
- BCFtools
- bcgTree
- bcl-convert
- bcl2fastq2
- bcolz
- bcrypt
- BDBag
- Beagle
- beagle-lib
- Beast
- BeautifulSoup
- BEDOPS
- BEDTools
- BEEF
- behave
- bench
- BerkeleyGW
- BFAST
- BFC
- BGC-Bayesian-genomic-clines
- BgeeCall
- BgeeDB
- bgen
- BGEN-enkre
- bgen-reader
- BiasAdjustCXX
- bibtexparser
- BiG-SCAPE
- BigDFT
- BinSanity
- binutils
- Bio-DB-HTS
- Bio-EUtilities
- Bio-FeatureIO
- Bio-SamTools
- Bio-SearchIO-hmmer
- bioawk
- biobakery-workflows
- biobambam2
- biogeme
- biom-format
- biomart-perl
- BioPerl
- BioPP
- Biopython
- BioServices
- Biotite
- BirdNET
- biscuit
- Bismark
- Bison
- bitarray
- bitsandbytes
- bitshuffle
- BLACS
- BLASR
- blasr_libcpp
- BLAST
- BLAST+
- BLAT
- Blender
- BLIS
- bliss
- Blitz++
- BlobTools
- Block
- Blosc
- Blosc2
- BLT
- bmtagger
- BMTK
- bnpy
- BOINC
- bokeh
- BoltzTraP
- BoltzTraP2
- Bonito
- Bonmin
- Bonnie++
- Boost
- Boost.MPI
- Boost.Python
- Boost.Python-NumPy
- boost_histogram
- BOPTEST
- boto3
- Bottleneck
- Bowtie
- Bowtie2
- Bpipe
- bpp
- bpytop
- Bracken
- Braindecode
- BRAKER
- BreakDancer
- breseq
- BRiAl
- Brotli
- Brotli-python
- Brunsli
- bsddb3
- BSMAPz
- Bsoft
- BSseeker2
- btllib
- BuDDy
- BUFRLIB
- build
- buildenv
- buildingspy
- Bullet
- BUSCO
- BUStools
- BWA
- bwa-mem2
- bwa-meth
- bwakit
- bwidget
- BWISE
- bx-python
- BXH_XCEDE_TOOLS
- byacc
- byobu
- bzip2
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BA3-SNPS-autotune/","title":"BA3-SNPS-autotune","text":"This program will automatically tune mixing parameters for BA3-SNPs by implementing a binary search algorithm and conducting short exploratory runs of BA3-SNPS.
homepage: https://github.com/stevemussmann/BA3-SNPS-autotune
version toolchain 2.1.2 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BAGEL/","title":"BAGEL","text":"BAGEL (Brilliantly Advanced General Electronic-structure Library) is a parallel electronic-structure program.
homepage: http://www.nubakery.org
version toolchain 1.1.1 intel/2016b 1.2.2 foss/2021a 1.2.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BAMM/","title":"BAMM","text":"BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution.
homepage: http://bamm-project.org/
version toolchain 2.5.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BAMSurgeon/","title":"BAMSurgeon","text":"Tools for adding mutations to existing .bam files, used for testing mutation callers
homepage: https://github.com/adamewing/bamsurgeon
version versionsuffix toolchain 1.2 -Python-2.7.16 GCC/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BAli-Phy/","title":"BAli-Phy","text":"BAli-Phy estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences.
homepage: http://www.bali-phy.org/
version toolchain 3.6.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BBMap/","title":"BBMap","text":"BBMap short read aligner, and other bioinformatic tools.
homepage: https://sourceforge.net/projects/bbmap/
version versionsuffix toolchain 36.62 -Java-1.8.0_112 intel/2016b 37.93 foss/2018a 37.93 intel/2018a 38.26 foss/2018b 38.50b GCC/8.2.0-2.31.1 38.76 GCC/8.2.0-2.31.1 38.79 GCC/8.3.0 38.87 GCC/8.2.0-2.31.1 38.87 iccifort/2020.1.217 38.90 GCC/10.2.0 38.90 GCC/9.3.0 38.96 GCC/10.3.0 38.98 GCC/11.2.0 39.01 GCC/11.3.0 39.01 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BCALM/","title":"BCALM","text":"de Bruijn graph compaction in low memory
homepage: https://github.com/GATB/bcalm
version toolchain 2.2.0 foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BCEL/","title":"BCEL","text":"The Byte Code Engineering Library (Apache Commons BCEL\u2122) is intended to give users a convenient way to analyze, create, and manipulate (binary) Java class files (those ending with .class).
homepage: http://commons.apache.org/proper/commons-bcel/
version versionsuffix toolchain 5.2 -Java-1.8 system 6.5.0 -Java-1.8 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BCFtools/","title":"BCFtools","text":"Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
homepage: https://www.htslib.org/
version toolchain 1.10.2 GCC/8.3.0 1.10.2 GCC/9.3.0 1.10.2 iccifort/2019.5.281 1.11 GCC/10.2.0 1.12 GCC/10.2.0 1.12 GCC/10.3.0 1.12 GCC/9.3.0 1.14 GCC/11.2.0 1.15.1 GCC/11.3.0 1.17 GCC/12.2.0 1.18 GCC/12.3.0 1.19 GCC/13.2.0 1.3 foss/2016a 1.3 intel/2016a 1.3.1 foss/2016b 1.6 foss/2016b 1.6 foss/2017b 1.6 intel/2017b 1.8 GCC/6.4.0-2.28 1.9 foss/2018a 1.9 foss/2018b 1.9 iccifort/2019.1.144-GCC-8.2.0-2.31.1 1.9 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BDBag/","title":"BDBag","text":"The bdbag utilities are a collection of software programs for working with BagIt packages that conform to the Bagit and Bagit/RO profiles.
homepage: https://github.com/fair-research/bdbag
version versionsuffix toolchain 1.4.1 -Python-2.7.14 intel/2018a 1.4.1 -Python-3.6.4 intel/2018a 1.6.3 intel/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BEDOPS/","title":"BEDOPS","text":"BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.
homepage: https://github.com/bedops/bedops
version toolchain 2.4.1 GCC/4.8.4 2.4.2 GCC/4.8.2 2.4.20 system 2.4.26 system 2.4.30 foss/2016b 2.4.32 foss/2018a 2.4.32 intel/2018a 2.4.35 foss/2018b 2.4.41 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BEDTools/","title":"BEDTools","text":"The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.
homepage: https://github.com/arq5x/bedtools2
version toolchain 2.25.0 foss/2016a 2.26.0 GCCcore/6.4.0 2.26.0 foss/2016a 2.26.0 intel/2016b 2.26.0 intel/2017a 2.26.0 intel/2017b 2.27.1 GCCcore/6.4.0 2.27.1 foss/2016b 2.27.1 foss/2018b 2.27.1 intel/2017a 2.27.1 intel/2018a 2.28.0 GCC/8.2.0-2.31.1 2.28.0 foss/2018b 2.28.0 iccifort/2019.1.144-GCC-8.2.0-2.31.1 2.29.2 GCC/8.3.0 2.29.2 GCC/9.3.0 2.30.0 GCC/10.2.0 2.30.0 GCC/10.3.0 2.30.0 GCC/11.2.0 2.30.0 GCC/11.3.0 2.30.0 GCC/12.2.0 2.30.0 iccifort/2020.4.304 2.31.0 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BEEF/","title":"BEEF","text":"BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149.
homepage: https://confluence.slac.stanford.edu/display/SUNCAT/BEEF+Functional+Software
version toolchain 0.1.1 iccifort/2019.5.281 0.1.1 iccifort/2020.4.304 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BFAST/","title":"BFAST","text":"BFAST facilitates the fast and accurate mapping of short reads to reference sequences. Some advantages of BFAST include: 1) Speed: enables billions of short reads to be mapped quickly. 2) Accuracy: A priori probabilities for mapping reads with defined set of variants. 3) An easy way to measurably tune accuracy at the expense of speed.
homepage: http://bfast.sourceforge.net/
version toolchain 0.7.0a foss/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BFC/","title":"BFC","text":"BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes.
homepage: https://github.com/lh3/bfc
version toolchain 1 foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BGC-Bayesian-genomic-clines/","title":"BGC-Bayesian-genomic-clines","text":"Collection of code for Bayesian genomic cline analyses.
homepage: https://github.com/zgompert/BGC-Bayesian-genomic-clines
version toolchain 1.03 gompi/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BGEN-enkre/","title":"BGEN-enkre","text":"This repository contains a reference implementation of the BGEN format, written in C++. The library can be used as the basis for BGEN support in other software, or as a reference for developers writing their own implementations of the BGEN format. Please cite: Band, G. and Marchini, J., \"BGEN: a binary file format for imputed genotype and haplotype data\", bioArxiv 308296; doi: https://doi.org/10.1101/308296
homepage: https://enkre.net/cgi-bin/code/bgen/dir?ci=trunk
version toolchain 1.1.7 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BLACS/","title":"BLACS","text":"The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms.
homepage: http://www.netlib.org/blacs/
version toolchain 1.1 gmvapich2/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BLASR/","title":"BLASR","text":"BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.
homepage: https://github.com/PacificBiosciences/blasr
version toolchain 2.2 intel/2016b 20170330 intel/2017a 5.3.3 gompi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BLAST%2B/","title":"BLAST+","text":"Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
homepage: https://blast.ncbi.nlm.nih.gov/
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","boost":0.5},{"location":"version-specific/supported-software/b/BLAST/","title":"BLAST","text":"Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
homepage: https://blast.ncbi.nlm.nih.gov/
version versionsuffix toolchain 2.10.0 -Linux_x86_64 system 2.10.1 -Linux_x86_64 system 2.11.0 -Linux_x86_64 system 2.2.26 -Linux_x86_64 system 2.8.1 -Linux_x86_64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BLAT/","title":"BLAT","text":"BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
homepage: https://genome.ucsc.edu/FAQ/FAQblat.html
version toolchain 3.5 GCC/8.2.0-2.31.1 3.5 GCC/8.3.0 3.5 GCC/9.3.0 3.5 foss/2016b 3.5 foss/2018b 3.5 intel/2016b 3.5 intel/2017a 3.7 GCC/10.3.0 3.7 GCC/11.2.0 3.7 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BLIS/","title":"BLIS","text":"BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.
homepage: https://github.com/flame/blis/
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","boost":0.5},{"location":"version-specific/supported-software/b/BLT/","title":"BLT","text":"BLT is an extension to the Tk toolkit, adding new widgets, geometry managers, and miscellaneous commands.
homepage: http://blt.sourceforge.net/
version toolchain 20181223 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BMTK/","title":"BMTK","text":"The Brain Modeling Toolkit (BMTK) is a python-based software package for building, simulating and analyzing large-scale neural network models. It supports the building and simulation of models of varying levels-of-resolution; from multi-compartment biophysically detailed networks, to point-neuron models, to filter-based models, and even population-level firing rate models.
homepage: https://alleninstitute.github.io/bmtk/index.html
version toolchain 1.0.8 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BOINC/","title":"BOINC","text":"BOINC is a program that lets you donate your idle computer time to science projects like SETI@home, Climateprediction.net, Rosetta@home, World Community Grid, and many others.
homepage: https://boinc.berkeley.edu
version versionsuffix toolchain 7.2.42 -client GCC/4.8.2 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BOPTEST/","title":"BOPTEST","text":"This repository contains code for the Building Optimization Performance Test framework (BOPTEST) that is being developed as part of the IBPSA Project 1.
homepage: https://ibpsa.github.io/project1-boptest/
version toolchain 0.3.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BRAKER/","title":"BRAKER","text":"BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes.
homepage: https://github.com/Gaius-Augustus/BRAKER
version versionsuffix toolchain 2.1.2 intel/2019a 2.1.5 -Python-3.7.4 intel/2019b 2.1.6 foss/2021b 2.1.6 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BRiAl/","title":"BRiAl","text":"BRiAl is the legacy version of PolyBoRi maintained by sagemath developers.
homepage: https://github.com/BRiAl/BRiAl
version toolchain 1.2.12 GCC/11.3.0 1.2.12 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BSMAPz/","title":"BSMAPz","text":"Updated and optimized fork of BSMAP. BSMAPz is a short reads mapping program for bisulfite sequencing in DNA methylation study.
homepage: https://github.com/zyndagj/BSMAPz
version versionsuffix toolchain 1.1.1 -Python-2.7.16 intel/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BSseeker2/","title":"BSseeker2","text":"BS-Seeker2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated reads.
homepage: http://pellegrini-legacy.mcdb.ucla.edu/bs_seeker2
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","boost":0.5},{"location":"version-specific/supported-software/b/BUFRLIB/","title":"BUFRLIB","text":"NCEP BUFRLIB software to encode or decode BUFR messages. It is not intended to be a primer on the BUFR code form itself.
homepage: https://www.emc.ncep.noaa.gov/index.php?branch=BUFRLIB
version toolchain 11.3.0.2 iccifort/2020.1.217 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BUSCO/","title":"BUSCO","text":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
homepage: http://busco.ezlab.org/
version versionsuffix toolchain 1.22 -Python-2.7.13 intel/2017a 2.0.1 -Python-2.7.13 intel/2017a 3.0.2 -Python-2.7.15 intel/2018b 4.0.5 -Python-3.7.4 foss/2019b 4.0.6 foss/2020b 5.0.0 foss/2020b 5.1.2 foss/2020b 5.4.2 foss/2021a 5.4.3 foss/2021b 5.4.5 foss/2022a 5.4.7 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BUStools/","title":"BUStools","text":"bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto | bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow.
homepage: https://github.com/BUStools/bustools
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","boost":0.5},{"location":"version-specific/supported-software/b/BWA/","title":"BWA","text":"Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
homepage: http://bio-bwa.sourceforge.net/
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","boost":0.5},{"location":"version-specific/supported-software/b/BWISE/","title":"BWISE","text":"de Bruijn Workflow using Integral information of Short pair End reads
homepage: https://github.com/Malfoy/BWISE
version versionsuffix toolchain 20180820 -Python-3.6.4 foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BXH_XCEDE_TOOLS/","title":"BXH_XCEDE_TOOLS","text":"A collection of data processing and image analysis tools for data in BXH or XCEDE format. This includes data format encapsulation/conversion, event-related analysis, QA tools, and more. These tools form the basis of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts.
homepage: http://www.nitrc.org/projects/bxh_xcede_tools/
version toolchain 1.11.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BabelStream/","title":"BabelStream","text":"STREAM, for lots of devices written in many programming models
homepage: https://uob-hpc.github.io/BabelStream
version versionsuffix toolchain 3.4 -omp GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/Bader/","title":"Bader","text":"A fast algorithm for doing Bader's analysis on a charge density grid.
homepage: http://theory.cm.utexas.edu/henkelman/code/bader/
version toolchain 1.02 intel/2018a 1.03 intel/2018b 1.04 GCC/11.2.0 1.04 iccifort/2020.4.304 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BamTools/","title":"BamTools","text":"BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
homepage: https://github.com/pezmaster31/bamtools
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","boost":0.5},{"location":"version-specific/supported-software/b/BamUtil/","title":"BamUtil","text":"BamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.
homepage: http://genome.sph.umich.edu/wiki/BamUtil
version toolchain 1.0.13 intel/2016b 1.0.14 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/Bambi/","title":"Bambi","text":"Bambi is a high-level Bayesian model-building interface written in Python. It works with the probabilistic programming frameworks PyMC3 and is designed to make it extremely easy to fit Bayesian mixed-effects models common in biology, social sciences and other disciplines.
homepage: https://bambinos.github.io/bambi
version toolchain 0.7.1 foss/2021b 0.7.1 intel/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/Bandage/","title":"Bandage","text":"Bandage is a program for visualising de novo assembly graphs
homepage: http://rrwick.github.io/Bandage/
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","boost":0.5},{"location":"version-specific/supported-software/b/Bash/","title":"Bash","text":"Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh).
homepage: http://www.gnu.org/software/bash
version toolchain 4.3 GCC/4.9.2 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BatMeth2/","title":"BatMeth2","text":"An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping.
homepage: https://github.com/GuoliangLi-HZAU/BatMeth2
version toolchain 2.1 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BayeScEnv/","title":"BayeScEnv","text":"BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation.
homepage: https://github.com/devillemereuil/bayescenv
version toolchain 1.1 GCC/8.3.0 1.1 foss/2016a 1.1 iccifort/2019.5.281 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BayeScan/","title":"BayeScan","text":"BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.
homepage: http://cmpg.unibe.ch/software/BayeScan/
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","boost":0.5},{"location":"version-specific/supported-software/b/BayesAss/","title":"BayesAss","text":"BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes
homepage: http://www.rannala.org/?page_id=245
version toolchain 3.0.4 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BayesAss3-SNPs/","title":"BayesAss3-SNPs","text":"Modification of BayesAss 3.0.4 to allow handling of large SNP datasets generated via methods such as RADseq protocols.
homepage: https://github.com/stevemussmann/BayesAss3-SNPs
version toolchain 1.1 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BayesOpt/","title":"BayesOpt","text":"BayesOpt is an efficient implementation of the Bayesian optimization methodology for nonlinear-optimization, experimental design, stochastic bandits and hyperparameter tunning
homepage: https://rmcantin.github.io/bayesopt
version toolchain 0.9 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BayesPrism/","title":"BayesPrism","text":"Bayesian cell Proportion Reconstruction Inferred using Statistical Marginalization (BayesPrism): A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
homepage: https://github.com/Danko-Lab/BayesPrism
version versionsuffix toolchain 2.0 -R-4.2.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BayesTraits/","title":"BayesTraits","text":"BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. This new package incoporates our earlier and separate programes Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits.
homepage: http://www.evolution.reading.ac.uk/BayesTraitsV1.html
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","boost":0.5},{"location":"version-specific/supported-software/b/Bazel/","title":"Bazel","text":"Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.
homepage: http://bazel.io/
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","boost":0.5},{"location":"version-specific/supported-software/b/Beagle/","title":"Beagle","text":"Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
homepage: https://faculty.washington.edu/browning/beagle/beagle.html
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","boost":0.5},{"location":"version-specific/supported-software/b/Beast/","title":"Beast","text":"BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.
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","boost":0.5},{"location":"version-specific/supported-software/b/BeautifulSoup/","title":"BeautifulSoup","text":"Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping.
homepage: https://www.crummy.com/software/BeautifulSoup
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","boost":0.5},{"location":"version-specific/supported-software/b/BerkeleyGW/","title":"BerkeleyGW","text":"The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.
homepage: http://www.berkeleygw.org
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","boost":0.5},{"location":"version-specific/supported-software/b/BgeeCall/","title":"BgeeCall","text":"Automatic RNA-Seq present/absent gene expression calls generation
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","boost":0.5},{"location":"version-specific/supported-software/b/BgeeDB/","title":"BgeeDB","text":"Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology.
homepage: https://github.com/BgeeDB/BgeeDB_R
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","boost":0.5},{"location":"version-specific/supported-software/b/BiG-SCAPE/","title":"BiG-SCAPE","text":"BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.
homepage: https://bigscape-corason.secondarymetabolites.org/index.html
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","boost":0.5},{"location":"version-specific/supported-software/b/BiasAdjustCXX/","title":"BiasAdjustCXX","text":"BiasAdjustCXX command-line tool for the application of fast and efficient bias corrections in climatic research
homepage: https://biasadjustcxx.readthedocs.io/en/latest/
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","boost":0.5},{"location":"version-specific/supported-software/b/BigDFT/","title":"BigDFT","text":"BigDFT: electronic structure calculation based on Daubechies wavelets. bigdft-suite is a set of different packages to run bigdft.
homepage: https://gitlab.com/l_sim/bigdft-suite
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","boost":0.5},{"location":"version-specific/supported-software/b/BinSanity/","title":"BinSanity","text":"BinSanity contains a suite a scripts designed to cluster contigs generated from metagenomic assembly into putative genomes.
homepage: https://github.com/edgraham/BinSanity/wiki
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","boost":0.5},{"location":"version-specific/supported-software/b/Boost/","title":"Boost","text":"Boost provides free peer-reviewed portable C++ source libraries.
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","boost":0.5},{"location":"version-specific/supported-software/b/Bottleneck/","title":"Bottleneck","text":"Fast NumPy array functions written in C
homepage: https://kwgoodman.github.io/bottleneck-doc
version versionsuffix toolchain 1.2.1 -Python-3.6.4 intel/2018a 1.3.2 -Python-3.8.2 foss/2020a 1.3.6 foss/2022a 1.3.7 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/Bowtie/","title":"Bowtie","text":"Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.
homepage: http://bowtie-bio.sourceforge.net/index.shtml
version toolchain 1.1.2 GCCcore/5.4.0 1.1.2 GCCcore/6.3.0 1.1.2 foss/2016a 1.1.2 intel/2016b 1.1.2 intel/2017a 1.1.2 intel/2018a 1.2.1.1 foss/2016b 1.2.1.1 intel/2017b 1.2.2 foss/2018b 1.2.2 intel/2017b 1.2.2 intel/2018a 1.2.3 GCC/8.2.0-2.31.1 1.2.3 GCC/8.3.0 1.2.3 GCC/9.3.0 1.2.3 foss/2018b 1.2.3 iccifort/2019.1.144-GCC-8.2.0-2.31.1 1.2.3 iccifort/2019.5.281 1.3.0 GCC/10.2.0 1.3.0 GCC/9.3.0 1.3.1 GCC/10.3.0 1.3.1 GCC/11.2.0 1.3.1 GCC/11.3.0 1.3.1 GCC/12.2.0 1.3.1 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/Bowtie2/","title":"Bowtie2","text":"Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
version toolchain 2.2.8 foss/2016a 2.2.9 foss/2016a 2.2.9 intel/2016b 2.3.2 foss/2016b 2.3.2 foss/2017a 2.3.2 intel/2017a 2.3.3.1 intel/2017b 2.3.4 intel/2017b 2.3.4.1 foss/2017b 2.3.4.1 intel/2017b 2.3.4.1 intel/2018a 2.3.4.2 foss/2018b 2.3.4.2 intel/2018b 2.3.4.3 foss/2017b 2.3.5.1 GCC/8.2.0-2.31.1 2.3.5.1 GCC/8.3.0 2.3.5.1 iccifort/2019.1.144-GCC-8.2.0-2.31.1 2.3.5.1 iccifort/2019.5.281 2.4.1 GCC/9.3.0 2.4.2 GCC/10.2.0 2.4.2 GCC/9.3.0 2.4.4 GCC/10.3.0 2.4.4 GCC/11.2.0 2.4.5 GCC/11.3.0 2.5.1 GCC/10.3.0 2.5.1 GCC/12.2.0 2.5.1 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/Bpipe/","title":"Bpipe","text":"Bpipe - a tool for running and managing bioinformatics pipelines
homepage: http://docs.bpipe.org/
version toolchain 0.9.9.2 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/Bracken/","title":"Bracken","text":"Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length.
homepage: https://ccb.jhu.edu/software/bracken/
version toolchain 2.6.0 GCCcore/9.3.0 2.6.2 GCCcore/11.2.0 2.7 GCCcore/11.2.0 2.9 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/Braindecode/","title":"Braindecode","text":"Braindecode is an open-source Python toolbox for decoding raw electrophysiological brain data with deep learning models. It includes dataset fetchers, data preprocessing and visualization tools, as well as implementations of several deep learning architectures and data augmentations for analysis of EEG, ECoG and MEG.
homepage: https://braindecode.org/
version versionsuffix toolchain 0.7 -PyTorch-1.10.0-CUDA-11.3.1 foss/2021a 0.7 -PyTorch-1.10.0 foss/2021a 0.8.1 -PyTorch-2.1.2-CUDA-12.1.1 foss/2023a 0.8.1 -PyTorch-2.1.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/BreakDancer/","title":"BreakDancer","text":"BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads
homepage: http://gmt.genome.wustl.edu/packages/breakdancer
version toolchain 1.4.5 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/Brotli-python/","title":"Brotli-python","text":"Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932.
homepage: https://github.com/google/brotli
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","boost":0.5},{"location":"version-specific/supported-software/b/Brotli/","title":"Brotli","text":"Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932.
homepage: https://github.com/google/brotli
version toolchain 1.0.9 GCCcore/10.2.0 1.0.9 GCCcore/10.3.0 1.0.9 GCCcore/11.2.0 1.0.9 GCCcore/11.3.0 1.0.9 GCCcore/12.2.0 1.0.9 GCCcore/12.3.0 1.0.9 GCCcore/8.3.0 1.1.0 GCCcore/13.2.0 1.1.0 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/Brunsli/","title":"Brunsli","text":"Brunsli is a lossless JPEG repacking library.
homepage: https://github.com/google/brunsli/
version toolchain 0.1 GCCcore/10.2.0 0.1 GCCcore/10.3.0 0.1 GCCcore/11.3.0 0.1 GCCcore/12.2.0 0.1 GCCcore/12.3.0 0.1 GCCcore/13.2.0 0.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/Bsoft/","title":"Bsoft","text":"Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages.
homepage: https://lsbr.niams.nih.gov/bsoft/
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","boost":0.5},{"location":"version-specific/supported-software/b/BuDDy/","title":"BuDDy","text":"A Binary Decision Diagram library, with many highly efficient vectorized BDD operations, dynamic variable reordering, automated garbage collection, a C++ interface with automatic reference counting, and much more.
homepage: http://buddy.sourceforge.net/
version toolchain 2.4 GCCcore/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/Bullet/","title":"Bullet","text":"Bullet professional 3D Game Multiphysics Library provides state of the art collision detection, soft body and rigid body dynamics.
homepage: http://bulletphysics.org/
version toolchain 2.83.7 foss/2016a 2.83.7 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/babl/","title":"babl","text":"babl is pixel encoding and color space conversion engine in C
homepage: https://www.gegl.org/babl
version toolchain 0.1.86 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bam-readcount/","title":"bam-readcount","text":"Count DNA sequence reads in BAM files
homepage: https://github.com/genome/bam-readcount
version toolchain 0.8.0 GCC/11.2.0 0.8.0 GCC/9.3.0 0.8.0 foss/2018b 1.0.1 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bamFilters/","title":"bamFilters","text":"A utility tool to filter alignments from bam files, using identity percent, low complexity and read coverage.
homepage: https://github.com/institut-de-genomique/bamFilters
version toolchain 2022-06-30 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bamtofastq/","title":"bamtofastq","text":"Convert 10x BAM files to the original FASTQs compatible with 10x pipelines.
homepage: https://github.com/10XGenomics/bamtofastq
version toolchain 1.4.0 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/barrnap/","title":"barrnap","text":"Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes.
homepage: https://github.com/tseemann/barrnap
version toolchain 0.9 GCC/8.2.0-2.31.1 0.9 foss/2018b 0.9 gompi/2020b 0.9 gompi/2021b 0.9 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/basemap/","title":"basemap","text":"The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python
homepage: http://matplotlib.org/basemap/
version versionsuffix toolchain 1.0.7 -Python-2.7.13 intel/2017a 1.0.7 -Python-3.6.3 intel/2017b 1.0.7 -Python-3.6.4 intel/2018a 1.2.0 -Python-3.6.6 intel/2018b 1.2.2 -Python-3.8.2 foss/2020a 1.3.6 foss/2022a 1.3.9 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bases2fastq/","title":"bases2fastq","text":"Bases2Fastq Software demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis with the FASTQ-compatible software of your choice. The Element AVITI\u2122 System records base calls, which are the main output of a sequencing run, with associated quality scores (Q-scores) in bases files. Bases files must be converted into the FASTQ file format for secondary analysis. To generate QC reports, also load BeautifulSoup and bokeh.
homepage: https://docs.elembio.io/docs/bases2fastq
version toolchain 1.5.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bashplotlib/","title":"bashplotlib","text":"bashplotlib is a python package and command line tool for making basic plots in the terminal. It's a quick way to visualize data when you don't have a GUI.
homepage: https://github.com/glamp/bashplotlib
version toolchain 0.6.5 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bat/","title":"bat","text":"The BAT Python package supports the processing and analysis of Bro data with Pandas, scikit-learn, and Spark
homepage: https://pypi.python.org/pypi/bat
version versionsuffix toolchain 0.3.3 -Python-3.6.3 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/batchgenerators/","title":"batchgenerators","text":"Data augmentation toolkit developed at the Division of Medical Image Computing at the German Cancer Research Center (DKFZ) to suit all our deep learning data augmentation needs.
homepage: https://github.com/MIC-DKFZ/batchgenerators
version toolchain 0.25 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bayesian-optimization/","title":"bayesian-optimization","text":"Pure Python implementation of bayesian global optimization with gaussian processes.
homepage: https://bayesian-optimization.github.io/BayesianOptimization/index.html
version toolchain 1.5.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bbFTP/","title":"bbFTP","text":"bbFTP is a file transfer software. It implements its own transfer protocol, which is optimized for large files (larger than 2GB) and secure as it does not read the password in a file and encrypts the connection information. bbFTP main features are: * Encoded username and password at connection * SSH and Certificate authentication modules * Multi-stream transfer * Big windows as defined in RFC1323 * On-the-fly data compression * Automatic retry * Customizable time-outs * Transfer simulation * AFS authentication integration * RFIO interface
homepage: https://software.in2p3.fr/bbftp/
version toolchain 3.2.1 GCCcore/9.3.0 3.2.1 intel/2016a 3.2.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bbcp/","title":"bbcp","text":"BBCP is an alternative to Gridftp when transferring large amounts of data, capable of breaking up your transfer into multiple simultaneous transferring streams, thereby transferring data much faster than single-streaming utilities such as SCP and SFTP. See details at http://pcbunn.cithep.caltech.edu/bbcp/using_bbcp.htm or http://www.nics.tennessee.edu/computing-resources/data-transfer/bbcp
homepage: http://www.slac.stanford.edu/~abh/bbcp/
version versionsuffix toolchain 12.01.30.00.0 -amd64_linux26 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bc/","title":"bc","text":"bc is an arbitrary precision numeric processing language.
homepage: https://www.gnu.org/software/bc/
version toolchain 1.06.95 GCC/4.8.2 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bcbio-gff/","title":"bcbio-gff","text":"Read and write Generic Feature Format (GFF) with Biopython integration.
homepage: https://github.com/chapmanb/bcbb/tree/master/gff
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","boost":0.5},{"location":"version-specific/supported-software/b/bcgTree/","title":"bcgTree","text":"Automatized phylogenetic tree building from bacterial core genomes.
homepage: https://github.com/molbiodiv/bcgTree
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","boost":0.5},{"location":"version-specific/supported-software/b/bcl-convert/","title":"bcl-convert","text":"The Illumina BCL Convert v4.0 is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files.
homepage: https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html
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","boost":0.5},{"location":"version-specific/supported-software/b/bcl2fastq2/","title":"bcl2fastq2","text":"bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
homepage: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
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","boost":0.5},{"location":"version-specific/supported-software/b/bcolz/","title":"bcolz","text":"bcolz provides columnar, chunked data containers that can be compressed either in-memory and on-disk. Column storage allows for efficiently querying tables, as well as for cheap column addition and removal. It is based on NumPy, and uses it as the standard data container to communicate with bcolz objects, but it also comes with support for import/export facilities to/from HDF5/PyTables tables and pandas dataframes.
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","boost":0.5},{"location":"version-specific/supported-software/b/bcrypt/","title":"bcrypt","text":"Acceptable password hashing for your software and your servers (but you should really use argon2id or scrypt)
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","boost":0.5},{"location":"version-specific/supported-software/b/behave/","title":"behave","text":"behave: Behavior-driven development (or BDD) is an agile software development technique that encourages collaboration between developers, QA and non-technical or business participants in a software project.
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","boost":0.5},{"location":"version-specific/supported-software/b/bench/","title":"bench","text":"Tools to accurately benchmark and analyze execution times for R expressions.
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","boost":0.5},{"location":"version-specific/supported-software/b/bgen/","title":"bgen","text":"A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3.
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","boost":0.5},{"location":"version-specific/supported-software/b/bioawk/","title":"bioawk","text":"Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
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","boost":0.5},{"location":"version-specific/supported-software/b/biobakery-workflows/","title":"biobakery-workflows","text":"bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters. Quality control and statistical summary reports are automatically generated for most data types, which include 16S amplicons, metagenomes, and metatranscriptomes. Workflows are run directly from the command line and tasks can be imported to create your own custom workflows. The workflows and tasks are built with AnADAMA2 which allows for parallel task execution locally and in a grid compute environment.
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","boost":0.5},{"location":"version-specific/supported-software/b/biobambam2/","title":"biobambam2","text":"Tools for processing BAM files
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","boost":0.5},{"location":"version-specific/supported-software/b/biogeme/","title":"biogeme","text":"Biogeme is a open source Python package designed for the maximum likelihood estimation of parametric models in general, with a special emphasis on discrete choice models.
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homepage: https://github.com/bnpy/bnpy
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","boost":0.5},{"location":"version-specific/supported-software/b/buildenv/","title":"buildenv","text":"This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you can use to easily transition between toolchains when building your software. To query the variables being set please use: module show
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homepage: https://github.com/bwa-mem2/bwa-mem2
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","boost":0.5},{"location":"version-specific/supported-software/b/bwa-meth/","title":"bwa-meth","text":"Fast and accurante alignment of BS-Seq reads.
homepage: https://github.com/brentp/bwa-meth
version toolchain 0.2.2 iccifort/2019.1.144-GCC-8.2.0-2.31.1 0.2.2 iccifort/2019.5.281 0.2.6 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bwakit/","title":"bwakit","text":"Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping.
homepage: https://github.com/lh3/bwa/tree/master/bwakit
version versionsuffix toolchain 0.7.15 _x64-linux system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bwidget/","title":"bwidget","text":"The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.
homepage: https://core.tcl-lang.org/bwidget/home
version toolchain 1.9.13 GCCcore/8.2.0 1.9.14 GCCcore/10.2.0 1.9.14 GCCcore/8.3.0 1.9.14 GCCcore/9.3.0 1.9.15 GCCcore/11.2.0 1.9.15 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bx-python/","title":"bx-python","text":"The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses.
homepage: https://github.com/bxlab/bx-python
version versionsuffix toolchain 0.10.0 foss/2023a 0.7.4 -Python-2.7.12 foss/2016b 0.7.4 -Python-2.7.13 intel/2017a 0.8.1 -Python-2.7.14 intel/2018a 0.8.11 foss/2021a 0.8.13 foss/2021b 0.8.2 -Python-3.6.6 foss/2018b 0.8.4 foss/2019a 0.8.8 -Python-3.7.4 foss/2019b 0.8.9 -Python-3.8.2 foss/2020a 0.9.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/byacc/","title":"byacc","text":"Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler.
homepage: http://invisible-island.net/byacc/byacc.html
version toolchain 2.0.20240109 GCCcore/13.3.0 20160324 intel/2016a 20160606 foss/2016b 20160606 intel/2016b 20170709 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/byobu/","title":"byobu","text":"Byobu is an elegant enhancement of the otherwise functional, plain, practical GNU Screen. Byobu includes an enhanced profile, configuration utilities, and system status notifications for the GNU screen window manager as well as the Tmux terminal multiplexer
homepage: https://byobu.org
version toolchain 5.133 GCC/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/b/bzip2/","title":"bzip2","text":"bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
homepage: https://sourceware.org/bzip2
version toolchain 1.0.6 GCC/4.8.1 1.0.6 GCC/4.8.2 1.0.6 GCC/4.8.4 1.0.6 GCC/4.9.2 1.0.6 GCC/4.9.3-2.25 1.0.6 GCC/5.4.0-2.26 1.0.6 GCCcore/4.9.3 1.0.6 GCCcore/5.4.0 1.0.6 GCCcore/6.3.0 1.0.6 GCCcore/6.4.0 1.0.6 GCCcore/7.2.0 1.0.6 GCCcore/7.3.0 1.0.6 GCCcore/8.2.0 1.0.6 GNU/4.9.3-2.25 1.0.6 foss/2016.04 1.0.6 foss/2016a 1.0.6 foss/2016b 1.0.6 gimkl/2.11.5 1.0.6 gimkl/2017a 1.0.6 intel/2016.02-GCC-4.9 1.0.6 intel/2016a 1.0.6 intel/2016b 1.0.6 iomkl/2016.07 1.0.6 iomkl/2016.09-GCC-4.9.3-2.25 1.0.6 system 1.0.8 GCCcore/10.2.0 1.0.8 GCCcore/10.3.0 1.0.8 GCCcore/11.2.0 1.0.8 GCCcore/11.3.0 1.0.8 GCCcore/12.2.0 1.0.8 GCCcore/12.3.0 1.0.8 GCCcore/13.1.0 1.0.8 GCCcore/13.2.0 1.0.8 GCCcore/13.3.0 1.0.8 GCCcore/8.3.0 1.0.8 GCCcore/9.3.0 1.0.8 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/","title":"List of supported software (c)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- c-ares
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- CalculiX-CrunchiX
- Calendrical
- Calib
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- Cantera
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- Canvas
- CAP3
- CapnProto
- captum
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- Carma
- carputils
- Cartopy
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- CatBoost
- Catch2
- category_encoders
- CatLearn
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- causallift
- causalml
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- Cbc
- CBLAS
- ccache
- CCCL
- CCfits
- CCL
- cclib
- cctbx-base
- cctools
- CD-HIT
- CDAT
- cdbfasta
- CDBtools
- cddlib
- CDFlib
- cDNA_Cupcake
- CDO
- cdo-bindings
- cdsapi
- cell2location
- CellBender
- CellChat
- CellMix
- CellOracle
- Cellpose
- CellRanger
- CellRanger-ARC
- CellRanger-ATAC
- CellRank
- CellTypist
- CENSO
- centerline
- Centrifuge
- Cereal
- CESM-deps
- CFDEMcoupling
- cffi
- cfgrib
- CFITSIO
- cftime
- CGAL
- cget
- Cgl
- CGmapTools
- CGNS
- CharLS
- charm-gems
- CHASE
- Check
- CheckM
- CheckM-Database
- CheckM2
- Cheetah
- Chemaxon-Marvin
- chemprop
- CheMPS2
- CHERAB
- chewBBACA
- chi2comb
- Chimera
- ChimPipe
- ChIPseeker
- chopper
- Chromaprint
- chromVARmotifs
- cicero
- CIF2Cell
- cimfomfa
- CIRCexplorer
- CIRCexplorer2
- Circlator
- Circos
- Circuitscape
- CIRI
- CIRI-long
- CIRIquant
- cisTEM
- CITE-seq-Count
- Clair3
- Clang
- Clang-AOMP
- Clang-Python-bindings
- CLANS
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- Clarabel.rs
- CLEAR
- CLEASE
- CLHEP
- CliMetLab
- CLIP
- cliquer
- CLISP
- ClonalFrameML
- CLooG
- CloudCompare
- Clp
- CLUMPP
- Clustal-Omega
- ClustalW2
- Cluster-Buster
- ClusterShell
- CMake
- CMAverse
- CmdStanR
- cmocean
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- CMSeq
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- CNVkit
- CNVnator
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- code-server
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- CodingQuarry
- Cogent
- Coin
- CoinUtils
- ColabFold
- colorize
- colossalai
- COMEBin
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- CompareM
- Compass
- Compress-Raw-Zlib
- COMSOL
- Con3F
- conan
- CONCOCT
- Concorde
- ConcurrentVersionsSystem
- configparser
- configurable-http-proxy
- CONN
- connected-components-3d
- ConnectomeWorkbench
- contextily
- Control-FREEC
- cooler
- CoordgenLibs
- Coot
- CopyKAT
- core-counter
- Coreutils
- corner
- CORSIKA
- COSTA
- CoSymLib
- coverage
- cowsay
- coxeter
- CP2K
- CPB
- CPC2
- cpio
- CPLEX
- CPMD
- CPPE
- CppHeaderParser
- CppUnit
- cppy
- cppyy
- cppzmq
- cpu_features
- cram
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- cramtools
- CrayCCE
- CrayGNU
- CrayIntel
- CrayPGI
- crb-blast
- CREST
- CRF++
- CRISPR-DAV
- CRISPResso2
- Critic2
- cromwell
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- CrossMap
- CrossTalkZ
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- Crumble
- cryoCARE
- cryoDRGN
- crypt4gh
- cryptography
- CryptoMiniSat
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- CSB
- CSBDeep
- CSBLAST
- cscope
- csvkit
- ctags
- ctffind
- ctffind5
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- Cube
- CubeGUI
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- CUDA-Samples
- CUDAcompat
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(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/C3D/","title":"C3D","text":"Convert3D Medical Image Processing Tool
homepage: https://sourceforge.net/projects/c3d/
version toolchain 1.0.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CAFE5/","title":"CAFE5","text":"Software for Computational Analysis of gene Family Evolution The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa.
homepage: https://github.com/hahnlab/CAFE5
version toolchain 5.0.0 GCC/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CAMPARI/","title":"CAMPARI","text":"CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte Carlo and molecular dynamics in seamless fashion.
homepage: http://campari.sourceforge.net/V4/index.html
version toolchain 4.0 foss/2023a 4.0 intel/2020b 4.0 intel/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CAP3/","title":"CAP3","text":"CAP3 assembly program
homepage: http://seq.cs.iastate.edu/
version toolchain 20071221-intel-x86 system 20071221-intel-x86_64 system 20071221-opteron system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CASA/","title":"CASA","text":"CASA, the Common Astronomy Software Applications package, is the primary data processing software for the Atacama Large Millimeter/submillimeter Array (ALMA) and NSF's Karl G. Jansky Very Large Array (VLA), and is frequently used also for other radio telescopes. The CASA software can process data from both single-dish and aperture-synthesis telescopes, and one of its core functionalities is to support the data reduction and imaging pipelines for ALMA, VLA and the VLA Sky Survey (VLASS).
homepage: https://casa.nrao.edu/
version versionsuffix toolchain 6.5.5-21 -py3.8 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CASPR/","title":"CASPR","text":"Running CASPR is extremely easy and convenient to analyze CRIPR-Cas9 screens using pgRNAs.
homepage: https://judithbergada.github.io/CASPR
version toolchain 20200730 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CASTEP/","title":"CASTEP","text":"CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.
homepage: http://www.castep.org
version toolchain 21.1.1 CrayCCE/19.06 21.1.1 CrayGNU/19.06 21.1.1 foss/2019b 21.1.1 intel/2019b 21.1.1 iomkl/2019b 22.11 foss/2022a 23.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CAT-BAT/","title":"CAT-BAT","text":"Tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs).
homepage: https://github.com/dutilh/CAT
version toolchain 5.2.3 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CAVIAR/","title":"CAVIAR","text":"CAusal Variants Identication in Associated Regions. A statistical framework that quantifies the probability of each variant to be causal while allowing an arbitrary number of causal variants.
homepage: https://github.com/fhormoz/caviar
version toolchain 2.2-20190419 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CBLAS/","title":"CBLAS","text":"C interface to the BLAS
homepage: http://www.netlib.org/blas/
version toolchain 20110120 foss/2016b 20110120 intel/2019b 20110120 intel/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CCCL/","title":"CCCL","text":"CUDA C++ Core Libraries (header only)
homepage: https://github.com/NVIDIA/cccl
version versionsuffix toolchain 2.3.0 -CUDA-12.1.1 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CCL/","title":"CCL","text":"Clozure CL (often called CCL for short) is a free Common Lisp implementation with a long history. Some distinguishing features of the implementation include fast compilation speed, native threads, a precise, generational, compacting garbage collector, and a convenient foreign-function interface.
homepage: https://ccl.clozure.com/
version toolchain 1.11.5 system 1.12 GCCcore/9.3.0 1.12.1 GCCcore/10.3.0 1.12.2 GCCcore/11.3.0 1.12.2 GCCcore/12.3.0 1.12.2 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CCfits/","title":"CCfits","text":"CCfits is an object oriented interface to the cfitsio library. It is designed to make the capabilities of cfitsio available to programmers working in C++.
homepage: https://heasarc.gsfc.nasa.gov/fitsio/CCfits/
version toolchain 2.5 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CD-HIT/","title":"CD-HIT","text":"CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
homepage: http://weizhongli-lab.org/cd-hit/
version versionsuffix toolchain 4.6.4 -2015-0603 GNU/4.9.3-2.25 4.6.6 foss/2016b 4.6.8 foss/2018b 4.6.8 intel/2017a 4.6.8 intel/2018a 4.8.1 GCC/10.2.0 4.8.1 GCC/10.3.0 4.8.1 GCC/11.2.0 4.8.1 GCC/11.3.0 4.8.1 GCC/12.2.0 4.8.1 GCC/12.3.0 4.8.1 GCC/8.3.0 4.8.1 GCC/9.3.0 4.8.1 foss/2018b 4.8.1 iccifort/2019.5.281 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CDAT/","title":"CDAT","text":"CDAT is a powerful and complete front-end to a rich set of visual-data exploration and analysis capabilities well suited for data analysis problems.
homepage: https://github.com/CDAT/cdat
version versionsuffix toolchain 8.2.1 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CDBtools/","title":"CDBtools","text":"CDB (Constant DataBase) indexing and retrieval tools for FASTA files
homepage: http://compbio.dfci.harvard.edu/tgi
version toolchain 0.99 GCC/10.2.0 0.99 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CDFlib/","title":"CDFlib","text":"cdflib is a python module to read/write CDF (Common Data Format .cdf) files without needing to install the CDF NASA library.
homepage: https://github.com/MAVENSDC/cdflib
version toolchain 0.4.9 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CDO/","title":"CDO","text":"CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
homepage: https://code.zmaw.de/projects/cdo
version toolchain 1.7.2 intel/2016b 1.8.1 intel/2017a 1.9.1 intel/2017b 1.9.10 gompi/2019b 1.9.10 gompi/2020b 1.9.10 gompi/2021a 1.9.10 iimpi/2021b 1.9.2 intel/2017b 1.9.5 intel/2018a 1.9.5 intel/2018b 1.9.5 iomkl/2018b 1.9.8 intel/2019b 2.0.5 gompi/2021b 2.0.6 gompi/2022a 2.1.1 gompi/2021a 2.2.2 gompi/2023a 2.2.2 gompi/2023b 2.3.0 iimpi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CENSO/","title":"CENSO","text":"Commandline Energetic SOrting (CENSO) is a sorting algorithm for efficient evaluation of Structure Ensembles (SE). The input ensemble (or single structure) originating from a CREST[SQM/FF] run can be ranked by free energy at DFT level and/or geometries can be optimized using DFT.
homepage: https://xtb-docs.readthedocs.io/en/latest/CENSO_docs/censo.html
version toolchain 1.2.0 GCCcore/12.3.0 1.2.0 intel/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CESM-deps/","title":"CESM-deps","text":"CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states.
homepage: https://www.cesm.ucar.edu/models/cesm2/
version toolchain 2 foss/2018b 2 foss/2021b 2 foss/2022a 2 foss/2023a 2 intel/2018b 2 iomkl/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CFDEMcoupling/","title":"CFDEMcoupling","text":"CFDEMcoupling is an open source CFD-DEM engine. It provides the possibility to couple the DEM engine LIGGGHTS to a CFD framework.
homepage: https://www.cfdem.com/cfdemrcoupling-open-source-cfd-dem-framework
version toolchain 3.8.0 foss/2018a 3.8.0 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CFITSIO/","title":"CFITSIO","text":"CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
homepage: http://heasarc.gsfc.nasa.gov/fitsio/
version toolchain 3.38 foss/2016a 3.38 intel/2016a 3.41 GCCcore/5.4.0 3.41 GCCcore/6.3.0 3.41 intel/2016b 3.42 GCCcore/6.4.0 3.42 intel/2017b 3.45 GCCcore/7.3.0 3.45 intel/2018b 3.47 GCCcore/8.2.0 3.47 GCCcore/8.3.0 3.48 GCCcore/9.3.0 3.49 GCCcore/10.2.0 3.49 GCCcore/10.3.0 3.49 GCCcore/11.2.0 4.2.0 GCCcore/11.3.0 4.2.0 GCCcore/12.2.0 4.3.0 GCCcore/12.3.0 4.3.1 GCCcore/13.2.0 4.4.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CGAL/","title":"CGAL","text":"The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.
homepage: http://www.cgal.org/
version versionsuffix toolchain 4.11 -Python-2.7.14 foss/2017b 4.11 -Python-3.6.3 foss/2017b 4.11 -Python-2.7.13 intel/2017a 4.11 -Python-2.7.14 intel/2017b 4.11 -Python-3.6.3 intel/2017b 4.11.1 -Python-2.7.14 foss/2018a 4.11.1 -Python-3.6.4 foss/2018a 4.11.1 -Python-2.7.15 foss/2018b 4.11.1 -Python-3.6.6 foss/2018b 4.11.1 -Python-2.7.14 intel/2018a 4.14 -Python-3.7.2 foss/2019a 4.14 -Python-3.7.2 intel/2019a 4.14.1 -Python-2.7.16 foss/2019b 4.14.1 -Python-3.7.4 foss/2019b 4.14.1 -Python-3.7.4 intel/2019b 4.14.3 -Python-3.8.2 gompi/2020a 4.14.3 gompi/2021a 4.14.3 gompi/2021b 4.14.3 gompi/2022a 4.14.3 -Python-3.8.2 iimpi/2020a 4.14.3 iimpi/2021a 4.8 -Python-2.7.11 foss/2016a 4.8 -Python-2.7.11 intel/2016a 4.8.1 -Python-2.7.12 foss/2016b 4.8.1 foss/2016b 4.8.1 -Python-2.7.12 intel/2016b 4.8.1 intel/2016b 4.9 -Python-2.7.12 intel/2016b 4.9 -Python-2.7.13 intel/2017a 5.2 gompi/2020b 5.4 GCCcore/12.3.0 5.5.2 GCCcore/12.2.0 5.6 GCCcore/12.3.0 5.6.1 GCCcore/13.2.0 5.6.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CGNS/","title":"CGNS","text":"The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data.
homepage: https://cgns.github.io/
version toolchain 3.3.1 foss/2016b 4.1.0 intelcuda/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CGmapTools/","title":"CGmapTools","text":"Command-line Toolset for Bisulfite Sequencing Data Analysis
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version toolchain 0.1.2 intel/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CHASE/","title":"CHASE","text":"Case-control HAplotype Sharing analyses. Haplotype sharing analyses for genome-wide association studies.
homepage: http://people.duke.edu/~asallen/Software.html
version toolchain 20130626 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CHERAB/","title":"CHERAB","text":"CHERAB is a python library for forward modelling diagnostics based on spectroscopic plasma emission.
homepage: https://cherab.github.io/documentation/index.html
version versionsuffix toolchain 1.2.0 -Python-3.6.6 intel/2018b 1.3.0 foss/2020b 1.3.0 intel/2020b 1.4.0 foss/2020b 1.4.0 intel/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CIF2Cell/","title":"CIF2Cell","text":"CIF2Cell is a tool to generate the geometrical setup for various electronic structure codes from a CIF (Crystallographic Information Framework) file. The program currently supports output for a number of popular electronic structure programs, including ABINIT, ASE, CASTEP, CP2K, CPMD, CRYSTAL09, Elk, EMTO, Exciting, Fleur, FHI-aims, Hutsepot, MOPAC, Quantum Espresso, RSPt, Siesta, SPR-KKR, VASP. Also exports some related formats like .coo, .cfg and .xyz-files.
homepage: https://sourceforge.net/projects/cif2cell
version versionsuffix toolchain 1.2.10 -Python-2.7.16 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CIRCexplorer/","title":"CIRCexplorer","text":"CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset.
homepage: https://circexplorer2.readthedocs.io/
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","boost":0.5},{"location":"version-specific/supported-software/c/CIRCexplorer2/","title":"CIRCexplorer2","text":"CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset.
homepage: https://circexplorer2.readthedocs.io/
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","boost":0.5},{"location":"version-specific/supported-software/c/CIRI-long/","title":"CIRI-long","text":"Circular RNA Identification for Long-Reads Nanopore Sequencing Data
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version toolchain 1.0.2 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CIRI/","title":"CIRI","text":"CircRNA Identifier. A de novo circular RNA identification tool
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version versionsuffix toolchain 2.0.6 -Perl-5.26.0 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CIRIquant/","title":"CIRIquant","text":"CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data
homepage: https://github.com/bioinfo-biols/CIRIquant
version versionsuffix toolchain 1.1.2-20221201 -Python-2.7.18 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CITE-seq-Count/","title":"CITE-seq-Count","text":"A python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment.
homepage: https://github.com/Hoohm/CITE-seq-Count
version versionsuffix toolchain 1.4.3 -Python-3.6.6 foss/2018b 1.4.3 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CLANS/","title":"CLANS","text":"CLANS 2.0 is a Python-based program for clustering sequences in the 2D or 3D space, based on their sequence similarities. CLANS visualizes the dynamic clustering process and enables the user to interactively control it and explore the cluster map in various ways.
homepage: https://github.com/inbalpaz/CLANS
version toolchain 2.0.8 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CLAPACK/","title":"CLAPACK","text":"C version of LAPACK
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version toolchain 3.2.1 GCC/6.4.0-2.28 3.2.1 iccifort/2017.4.196-GCC-6.4.0-2.28 3.2.1 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CLEAR/","title":"CLEAR","text":"Direct comparison of circular and linear RNA expression
homepage: https://github.com/YangLab/CLEAR
version versionsuffix toolchain 20210117 -Python-2.7.18 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CLEASE/","title":"CLEASE","text":"CLuster Expansion in Atomic Simulation Environment (CLEASE) is a package that automates the cumbersome setup and construction procedure of cluster expansion (CE). It provides a comprehensive list of tools for specifying parameters for CE, generating training structures, fitting effective cluster interaction (ECI) values and running Monte Carlo simulations.
homepage: https://gitlab.com/computationalmaterials/clease
version toolchain 0.10.6 intel/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CLHEP/","title":"CLHEP","text":"The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package.
homepage: http://proj-clhep.web.cern.ch/proj-clhep/
version toolchain 2.1.1.0 intel/2016a 2.1.3.1 intel/2016a 2.2.0.8 intel/2016a 2.3.1.1 intel/2016a 2.3.4.3 foss/2017b 2.3.4.3 intel/2017b 2.4.0.0 intel/2017b 2.4.1.0 foss/2017b 2.4.1.0 foss/2018b 2.4.1.0 intel/2017b 2.4.1.0 intel/2018b 2.4.1.3 foss/2019b 2.4.1.3 foss/2020a 2.4.4.0 GCC/10.2.0 2.4.4.0 GCC/11.2.0 2.4.5.1 GCC/11.2.0 2.4.5.3 GCC/11.3.0 2.4.6.2 GCC/11.3.0 2.4.6.4 GCC/12.2.0 2.4.7.1 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CLIP/","title":"CLIP","text":"CLIP (Contrastive Language-Image Pre-Training) is a neural network trained on a variety of (image, text) pairs. It can be instructed in natural language to predict the most relevant text snippet, given an image, without directly optimizing for the task, similarly to the zero-shot capabilities of GPT-2 and 3.
homepage: https://github.com/openai/CLIP
version versionsuffix toolchain 20230220 -CUDA-11.7.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CLISP/","title":"CLISP","text":"Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language.
homepage: http://www.clisp.org/
version toolchain 2.49 GCCcore/6.4.0 2.49 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CLUMPP/","title":"CLUMPP","text":"CLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses.
homepage: https://rosenberglab.stanford.edu/clumpp.html
version versionsuffix toolchain 1.1.2 -Linux64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CLooG/","title":"CLooG","text":"CLooG is a free software and library to generate code for scanning Z-polyhedra. That is, it finds a code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra. CLooG has been originally written to solve the code generation problem for optimizing compilers based on the polytope model. Nevertheless it is used now in various area e.g. to build control automata for high-level synthesis or to find the best polynomial approximation of a function. CLooG may help in any situation where scanning polyhedra matters. While the user has full control on generated code quality, CLooG is designed to avoid control overhead and to produce a very effective code.
homepage: http://www.bastoul.net/cloog/index.php
version toolchain 0.18.1 GCC/4.8.2 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CMAverse/","title":"CMAverse","text":"The R package CMAverse provides a suite of functions for reproducible causal mediation analysis including cmdag for DAG visualization, cmest for statistical modeling and cmsens for sensitivity analysis.
homepage: https://bs1125.github.io/CMAverse/
version toolchain 20220112 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CMSeq/","title":"CMSeq","text":"CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus.
homepage: https://github.com/SegataLab/cmseq/
version versionsuffix toolchain 1.0.3 -Python-3.8.2 foss/2020a 1.0.4 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CMake/","title":"CMake","text":"CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
homepage: https://www.cmake.org
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","boost":0.5},{"location":"version-specific/supported-software/c/CNT-ILP/","title":"CNT-ILP","text":"Integer Linear Program for the Copy-Number Tree Problem
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version toolchain 20171031 GCC/8.2.0-2.31.1 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CNVkit/","title":"CNVkit","text":"A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.
homepage: https://github.com/etal/cnvkit
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","boost":0.5},{"location":"version-specific/supported-software/c/CNVnator/","title":"CNVnator","text":"a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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version toolchain 0.3.3 foss/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/COBRApy/","title":"COBRApy","text":"COBRApy is a package for constraint-based modeling of metabolic networks.
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","boost":0.5},{"location":"version-specific/supported-software/c/CODEX2/","title":"CODEX2","text":"Full-spectrum copy number variation detection by high-throughput DNA sequencing
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version versionsuffix toolchain 20180227 -R-3.4.3 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/COMEBin/","title":"COMEBin","text":"Effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning
homepage: https://github.com/ziyewang/COMEBin
version toolchain 1.0.3-20240310 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/COMSOL/","title":"COMSOL","text":"COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems.
homepage: https://www.comsol.com
version toolchain 5.4.0.225 system 6.2.0.290 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CONCOCT/","title":"CONCOCT","text":"Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.
homepage: https://concoct.readthedocs.io
version versionsuffix toolchain 1.0.0 -Python-2.7.14 foss/2017b 1.0.0 -Python-3.6.3 foss/2017b 1.0.0 -Python-2.7.15 foss/2018b 1.1.0 -Python-2.7.15 foss/2019a 1.1.0 -Python-2.7.18 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CONN/","title":"CONN","text":"CONN is an open-source Matlab/SPM-based cross-platform software for the computation, display, and analysis of functional connectivity Magnetic Resonance Imaging (fcMRI). CONN is used to analyze resting state data (rsfMRI) as well as task-related designs.
homepage: https://web.conn-toolbox.org/home
version versionsuffix toolchain 21a -MATLAB-2021a system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CORSIKA/","title":"CORSIKA","text":"CORSIKA (COsmic Ray SImulations for KAscade) is a program for detailed simulation of extensive air showers initiated by high energy cosmic ray particles. Protons, light nuclei up to iron, photons, and many other particles may be treated as primaries.
homepage: https://www.iap.kit.edu/corsika
version toolchain 77550 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/COSTA/","title":"COSTA","text":"OSTA is a communication-optimal, highly-optimised algorithm for data redistribution accross multiple processors, using MPI and OpenMP and offering the possibility to transpose and scale some or all data.
homepage: https://github.com/eth-cscs/COSTA
version toolchain 2.2.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CP2K/","title":"CP2K","text":"CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
homepage: https://www.cp2k.org/
version versionsuffix toolchain 2022.1 foss/2022a 2023.1 foss/2022b 2023.1 foss/2023a 3.0 intel/2016a 3.0 -psmp intel/2016b 3.0 intel/2016b 3.0 intel/2017b 3.0 intel/2018a 4.1 -psmp foss/2016b 4.1 intel/2016b 5.1 foss/2018a 5.1 foss/2020a 5.1 foss/2020b 5.1 intel/2017b 5.1 intel/2018a 5.1 intel/2020a 6.1 foss/2019a 6.1 intel/2018a 6.1 intel/2020a 7.1 foss/2020a 7.1 -psmp foss/2020b 7.1 foss/2020b 7.1 intel/2020a 7.1 intel/2020b 8.1 foss/2020b 8.2 foss/2021a 8.2 intel/2021a 9.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CPB/","title":"CPB","text":"CPB is a novel two-step Pearson correlation based biclustering approach to mine genes that are co-regulated with a given reference gene in order to discover genes that function in a common biological process. In the first step, the algorithm identifies subsets of genes with high correlation, reducing false negatives with a nonparametric filtering scheme. In the second step, biclusters from multiple datasets are used to extract and rank gene correlation information.
homepage: http://tda.gatech.edu/software/cpb/index.html
version versionsuffix toolchain 11-4-2011 -Python-2.7.13 foss/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CPC2/","title":"CPC2","text":"a fast and accurate coding potential calculator based on sequence intrinsic features
homepage: http://cpc2.gao-lab.org/
version toolchain 1.0.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CPLEX/","title":"CPLEX","text":"IBM ILOG CPLEX Optimizer's mathematical programming technology enables analytical decision support for improving efficiency, reducing costs, and increasing profitability.
homepage: https://www.ibm.com/analytics/cplex-optimizer
version versionsuffix toolchain 12.10 -Python-3.7.4 GCCcore/8.3.0 12.9 GCCcore/8.2.0 22.1.1 GCCcore/11.2.0 22.1.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CPMD/","title":"CPMD","text":"The CPMD code is a parallelized plane wave / pseudopotential implementation of DFT, particularly designed for ab-initio molecular dynamics.
homepage: https://github.com/CPMD-code
version toolchain 4.3 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CPPE/","title":"CPPE","text":"CPPE is an open-source, light-weight C++ and Python library for Polarizable Embedding (PE)1,2 calculations. It provides an easy-to-use API to implement PE for ground-state self-consistent field (SCF) calculations and post-SCF methods. A convenient Python interface is also available.
homepage: https://github.com/maxscheurer/cppe
version toolchain 0.3.1 GCC/11.3.0 0.3.1 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CREST/","title":"CREST","text":"CREST is an utility/driver program for the xtb program. Originally it was designed as conformer sampling program, hence the abbreviation Conformer\u2013Rotamer Ensemble Sampling Tool, but now offers also some utility functions for calculations with the GFNn\u2013xTB methods. Generally the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb program) and tool for the creation and analysation of structure ensembles.
homepage: https://xtb-docs.readthedocs.io/en/latest/crest.html
version toolchain 2.11 intel/2021a 2.11.2 intel/2021a 2.12 gfbf/2023a 2.12 gfbf/2023b 2.12 intel/2022a 3.0.1 gfbf/2022b 3.0.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CRF%2B%2B/","title":"CRF++","text":"CRF++ is a simple, customizable, and open source implementation of Conditional Random Fields (CRFs) for segmenting/labeling sequential data. CRF++ is designed for generic purpose and will be applied to a variety of NLP tasks, such as Named Entity Recognition, Information Extraction and Text Chunking.
homepage: https://taku910.github.io/crfpp/
version toolchain 0.58 iccifort/2019.1.144-GCC-8.2.0-2.31.1 0.58 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CRISPR-DAV/","title":"CRISPR-DAV","text":"CRISPR-DAV is a pipeline to analyze amplicon-based NGS data of CRISPR clones in a high throughput manner.
homepage: https://github.com/pinetree1/crispr-dav/
version toolchain 2.3.4 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CRISPResso2/","title":"CRISPResso2","text":"CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments.
homepage: https://github.com/pinellolab/CRISPResso2
version versionsuffix toolchain 2.0.44 -Python-2.7.16 foss/2019b 2.1.2 -Python-2.7.18 foss/2020b 2.2.1 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CRPropa/","title":"CRPropa","text":"CRPropa is a publicly available code to study the propagation of ultra high energy nuclei up to iron on their voyage through an extra galactic environment.
homepage: https://crpropa.desy.de
version versionsuffix toolchain 3.1.5 -Python-3.7.2 foss/2019a 3.1.6 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CSB/","title":"CSB","text":"Computational Structural Biology Toolbox CSB is a python library and application framework, which can be used to solve problems in the field of structural bioinformatics. If you are a bioinformatician, software engineer or a researcher working in this field, chances are you may find something useful here. Our package consists of a few major components: 1. Core class library - object-oriented, granular, with an emphasis on design and clean interfaces. 2. Application framework - console applications (\"protocols\"), which consume objects from the core library in order to build something executable (and hopefully useful). 3. Test framework - ensures that the library actually works.
homepage: https://github.com/csb-toolbox
version toolchain 1.2.5 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CSBDeep/","title":"CSBDeep","text":"CSBDeep is a toolbox for Content-aware Image Restoration (CARE).
homepage: https://csbdeep.bioimagecomputing.com/
version versionsuffix toolchain 0.4.1 -Python-3.7.2 foss/2019a 0.4.1 -Python-3.7.2 fosscuda/2019a 0.7.4 -CUDA-11.7.0 foss/2022a 0.7.4 foss/2022a 0.7.4 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CSBLAST/","title":"CSBLAST","text":"Context-specific extension of BLAST that significantly improves sensitivity and alignment quality.
homepage: https://github.com/soedinglab/csblast/
version toolchain 2.2.3 GCCcore/8.3.0 2.2.4 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CTPL/","title":"CTPL","text":"Modern and efficient C++ Thread Pool Library
homepage: https://github.com/vit-vit/CTPL.git
version toolchain 0.0.2 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CUDA-Samples/","title":"CUDA-Samples","text":"Samples for CUDA Developers which demonstrates features in CUDA Toolkit
homepage: https://github.com/NVIDIA/cuda-samples
version versionsuffix toolchain 11.3 -CUDA-11.3.1 GCC/10.3.0 11.6 -CUDA-11.7.0 GCC/11.3.0 11.8 -CUDA-11.7.0 GCC/11.3.0 12.1 -CUDA-12.1.1 GCC/12.3.0 12.2 -CUDA-12.2.0 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CUDA/","title":"CUDA","text":"CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
homepage: https://developer.nvidia.com/cuda-toolkit
version toolchain 10.0.130 system 10.1.105 GCC/8.2.0-2.31.1 10.1.105 iccifort/2019.1.144-GCC-8.2.0-2.31.1 10.1.105 system 10.1.168 system 10.1.243 GCC/8.3.0 10.1.243 iccifort/2019.5.281 10.1.243 system 10.2.89 GCC/8.3.0 11.0.2 GCC/9.3.0 11.0.2 iccifort/2020.1.217 11.1.1 GCC/10.2.0 11.1.1 iccifort/2020.4.304 11.3.1 system 11.4.1 system 11.4.2 system 11.5.0 system 11.5.1 system 11.5.2 system 11.6.0 system 11.7.0 system 11.8.0 system 12.0.0 system 12.1.0 system 12.1.1 system 12.2.0 system 12.2.2 system 12.3.0 system 12.3.2 system 12.4.0 system 12.5.0 system 12.6.0 system 5.5.22 GCC/4.8.2 5.5.22 system 6.0.37 system 6.5.14 system 7.0.28 system 7.5.18 GCC/4.9.4-2.25 7.5.18 iccifort/2016.3.210-GCC-4.9.3-2.25 7.5.18 system 8.0.44 GCC/5.4.0-2.26 8.0.44 iccifort/2016.3.210-GCC-5.4.0-2.26 8.0.44 system 8.0.61 system 8.0.61_375.26 GCC/5.4.0-2.26 9.0.176 GCC/6.4.0-2.28 9.0.176 iccifort/2017.4.196-GCC-6.4.0-2.28 9.0.176 system 9.1.85 GCC/6.4.0-2.28 9.1.85 system 9.2.148.1 system 9.2.88 GCC/6.4.0-2.28 9.2.88 GCC/7.3.0-2.30 9.2.88 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CUDAcompat/","title":"CUDAcompat","text":"Using the CUDA Forward Compatibility package, system administrators can run applications built using a newer toolkit even when an older driver that does not satisfy the minimum required driver version is installed on the system. This forward compatibility allows the CUDA deployments in data centers and enterprises to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit.
homepage: https://docs.nvidia.com/deploy/cuda-compatibility/index.html
version versionsuffix toolchain 11.6 -510.85.02 system 11.6 system 11.7 -515.65.01 system 11.7 system 11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CUDAcore/","title":"CUDAcore","text":"CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
homepage: https://developer.nvidia.com/cuda-toolkit
version toolchain 11.0.2 system 11.1.1 system 11.2.1 system 11.2.2 system 11.3.0 system 11.4.0 system 11.5.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CUDD/","title":"CUDD","text":"The CUDD package is a package written in C for the manipulation of decision diagrams. It supports binary decision diagrams (BDDs), algebraic decision diagrams (ADDs), and Zero-Suppressed BDDs (ZDDs).
homepage: https://github.com/ivmai/cudd
version toolchain 3.0.0 GCC/11.3.0 3.0.0 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CUTLASS/","title":"CUTLASS","text":"CUTLASS is a collection of CUDA C++ template abstractions for implementing high-performance matrix-matrix multiplication (GEMM) and related computations at all levels and scales within CUDA. It incorporates strategies for hierarchical decomposition and data movement similar to those used to implement cuBLAS and cuDNN. CUTLASS decomposes these \"moving parts\" into reusable, modular software components abstracted by C++ template classes. Primitives for different levels of a conceptual parallelization hierarchy can be specialized and tuned via custom tiling sizes, data types, and other algorithmic policy. The resulting flexibility simplifies their use as building blocks within custom kernels and applications.
homepage: https://github.com/NVIDIA/cutlass
version versionsuffix toolchain 2.11.0 -CUDA-11.7.0 foss/2022a 3.4.0 -CUDA-12.1.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CUnit/","title":"CUnit","text":"Automated testing framework for C.
homepage: https://sourceforge.net/projects/cunit/
version toolchain 2.1-3 GCCcore/11.2.0 2.1-3 GCCcore/11.3.0 2.1-3 GCCcore/12.3.0 2.1-3 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CVX/","title":"CVX","text":"CVX is a Matlab-based modeling system for convex optimization. CVX turns Matlab into a modeling language, allowing constraints and objectives to be specified using standard Matlab expression syntax.
homepage: https://cvxr.com/cvx/
version versionsuffix toolchain 2.2 -MATLAB-2023a system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CVXOPT/","title":"CVXOPT","text":"CVXOPT is a free software package for convex optimization based on the Python programming language. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Python's extensive standard library and on the strengths of Python as a high-level programming language.
homepage: http://cvxopt.org
version versionsuffix toolchain 1.1.9 -Python-2.7.13 intel/2017a 1.2.1 -Python-3.6.4 intel/2018a 1.2.3 foss/2019a 1.2.3 -Python-3.6.6 intel/2018b 1.2.4 -Python-3.7.4 intel/2019b 1.2.6 foss/2020b 1.2.6 foss/2021a 1.3.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CVXPY/","title":"CVXPY","text":"CVXPY is a Python-embedded modeling language for convex optimization problems. It allows you to express your problem in a natural way that follows the math, rather than in the restrictive standard form required by solvers.
homepage: https://www.cvxpy.org/
version versionsuffix toolchain 1.0.24 foss/2019a 1.0.28 -Python-3.7.4 foss/2019b 1.3.0 foss/2022a 1.4.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CVglasso/","title":"CVglasso","text":"CVglasso is an R package that estimates a lasso-penalized precision matrix via block-wise coordinate descent \u2013 also known as the graphical lasso (glasso) algorithm.
homepage: https://github.com/MGallow/CVglasso
version versionsuffix toolchain 1.0 -R-4.2.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CWIPI/","title":"CWIPI","text":"CWIPI (Coupling With Interpolation Parallel Interface) library helps in chaining and coupling codes. Provides exchanges of interpolated fields through a non-compliant geometric interface and allows control of the coupling algorithm using control parameters. CWIPI takes advantage of the distribution of the definition of the coupling algorithm in the different codes.
homepage: https://w3.onera.fr/cwipi/
version toolchain 0.12.0 gompi/2021a 0.12.0 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CaDiCaL/","title":"CaDiCaL","text":"CaDiCaL is a simplified satisfiability solver. The original goal of the development of CaDiCaL was to obtain a CDCL solver, which is easy to understand and change, while at the same time not being much slower than other state-of-the-art CDCL solvers.
homepage: https://github.com/arminbiere/cadical
version toolchain 1.3.0 GCC/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CaSpER/","title":"CaSpER","text":"CaSpER is a signal processing approach for identification, visualization, and integrative analysis of focal and large-scale CNV events in multiscale resolution using either bulk or single-cell RNA sequencing data.
homepage: https://github.com/akdess/CaSpER
version toolchain 2.0 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CaVEMan/","title":"CaVEMan","text":"SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib
homepage: http://cancerit.github.io/CaVEMan/
version toolchain 1.13.2 foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/Caffe/","title":"Caffe","text":"Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors.
homepage: https://github.com/BVLC/caffe
version versionsuffix toolchain 1.0 -Python-2.7.13 intel/2017a 1.0 -CUDA-9.1.85-Python-2.7.14 intel/2017b 1.0 -Python-2.7.14 intel/2017b rc3 -CUDA-7.5.18-Python-2.7.11 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/Calcam/","title":"Calcam","text":"Calcam is a Python package providing tools for spatial calibration of cameras, i.e. determining the mapping between pixel coordinates in an image and real-world 3D sight lines & coordinates.
homepage: https://euratom-software.github.io/calcam
version versionsuffix toolchain 2.1.0 -Python-2.7.14 intel/2018a 2.1.0 -Python-3.6.4 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CalculiX-CrunchiX/","title":"CalculiX-CrunchiX","text":"A Free Software Three-Dimensional Structural Finite Element Program
homepage: http://www.calculix.de
version toolchain 2.20 foss/2021a 2.20 foss/2022b 2.20 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/Calendrical/","title":"Calendrical","text":"Calendrical module is for calendrical calculations.
homepage: https://www.funaba.org/code#calendrical
version versionsuffix toolchain 2.0.1 -Python-3.6.3 intel/2017b 2.0.2a -Python-3.6.4 intel/2018a 2.0.2a -Python-3.6.6 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/Calib/","title":"Calib","text":"Calib clusters paired-end reads using their barcodes and sequences. Calib is suitable for amplicon sequencing where a molecule is tagged, then PCR amplified with high depth, also known as Unique Molecule Identifier (UMI) sequencing.
homepage: https://github.com/vpc-ccg/calib
version toolchain 0.3.4 GCC/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/Cantera/","title":"Cantera","text":"Chemical kinetics, thermodynamics, and transport tool suite
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","boost":0.5},{"location":"version-specific/supported-software/c/Circuitscape/","title":"Circuitscape","text":"Algorithms from circuit theory to predict connectivity in heterogeneous landscapes
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homepage: https://github.com/HKU-BAL/Clair3
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homepage: https://github.com/RadeonOpenCompute/llvm-project
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homepage: https://github.com/coin-or/Clp
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homepage: http://www.clustal.org/omega/
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homepage: https://github.com/weng-lab/cluster-buster/
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homepage: https://cea-hpc.github.io/clustershell/
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homepage: https://mc-stan.org/cmdstanr
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homepage: https://github.com/yhg926/co-phylog
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homepage: http://cocoa.dima.unige.it/cocoalib
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homepage: https://github.com/pedronachtigall/CodAn
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homepage: https://github.com/Magdoll/Cogent
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homepage: https://github.com/BoevaLab/FREEC
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version toolchain 1.12.1 GCCcore/6.4.0 1.12.1 GCCcore/7.3.0 1.12.1 foss/2016a 1.15.1 GCCcore/10.2.0 1.15.1 GCCcore/10.3.0 1.15.1 GCCcore/11.3.0 1.15.1 GCCcore/12.2.0 1.15.1 GCCcore/12.3.0 1.15.1 GCCcore/8.3.0 1.15.1 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CrayCCE/","title":"CrayCCE","text":"Toolchain using Cray compiler wrapper, using PrgEnv-cray (PE release: June 2019).
homepage: https://pubs.cray.com/discover
version toolchain 19.06 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CrayGNU/","title":"CrayGNU","text":"Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: June 2019).
homepage: https://pubs.cray.com/discover
version toolchain 19.06 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CrayIntel/","title":"CrayIntel","text":"Toolchain using Cray compiler wrapper, using PrgEnv-intel (PE release: June 2019).
homepage: https://pubs.cray.com/discover
version toolchain 19.06 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CrayPGI/","title":"CrayPGI","text":"Toolchain using Cray compiler wrapper, PrgEnv-pgi compiler (PE release: June 2019).
homepage: https://pubs.cray.com/discover
version toolchain 19.06 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/Critic2/","title":"Critic2","text":"Critic2 is a program for the analysis of quantum mechanical calculation results in molecules and periodic solids.
homepage: https://aoterodelaroza.github.io/critic2/
version toolchain 1.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CrossMap/","title":"CrossMap","text":"CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF and VCF.
homepage: http://crossmap.sourceforge.net
version versionsuffix toolchain 0.3.9 -Python-3.7.2 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CrossTalkZ/","title":"CrossTalkZ","text":"CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks.
homepage: http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/
version toolchain 1.4 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/Crumble/","title":"Crumble","text":"Exploration of controlled loss of quality values for compressing CRAM files
homepage: https://github.com/jkbonfield/crumble
version toolchain 0.8.3 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CryptoMiniSat/","title":"CryptoMiniSat","text":"CryptoMiniSat is an advanced SAT solver
homepage: https://github.com/msoos/cryptominisat
version versionsuffix toolchain 5.0.1 -Python-2.7.12 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CrystFEL/","title":"CrystFEL","text":"CrystFEL is a suite of programs for processing diffraction data acquired \"serially\" in a \"snapshot\" manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source.
homepage: http://www.desy.de/~twhite/crystfel/
version toolchain 0.8.0 foss/2019a 0.8.0 intel/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CuCLARK/","title":"CuCLARK","text":"Metagenomic classifier for CUDA-enabled GPUs
homepage: https://github.com/Funatiq/cuclark
version toolchain 1.1 fosscuda/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CuPy/","title":"CuPy","text":"CuPy is an open-source array library accelerated with NVIDIA CUDA.
homepage: https://cupy.dev
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","boost":0.5},{"location":"version-specific/supported-software/c/Cube/","title":"Cube","text":"Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity.
homepage: http://www.scalasca.org/software/cube-4.x/download.html
version toolchain 4.3.4 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CubeGUI/","title":"CubeGUI","text":"Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube graphical report explorer.
homepage: https://www.scalasca.org/software/cube-4.x/download.html
version toolchain 4.4.4 GCCcore/8.2.0 4.4.4 GCCcore/9.3.0 4.6 GCCcore/10.2.0 4.6 GCCcore/10.3.0 4.8 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CubeLib/","title":"CubeLib","text":"Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube general purpose C++ library component and command-line tools.
homepage: https://www.scalasca.org/software/cube-4.x/download.html
version toolchain 4.4.4 GCCcore/8.2.0 4.4.4 GCCcore/8.3.0 4.4.4 GCCcore/9.3.0 4.6 GCCcore/10.2.0 4.6 GCCcore/10.3.0 4.8 GCCcore/11.2.0 4.8 GCCcore/11.3.0 4.8.1 GCCcore/12.2.0 4.8.1 GCCcore/12.3.0 4.8.2 GCCcore/12.2.0 4.8.2 GCCcore/13.2.0 4.8.2 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/CubeWriter/","title":"CubeWriter","text":"Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube high-performance C writer library component.
homepage: https://www.scalasca.org/software/cube-4.x/download.html
version toolchain 4.4.3 GCCcore/10.2.0 4.4.3 GCCcore/8.2.0 4.4.3 GCCcore/8.3.0 4.4.3 GCCcore/9.3.0 4.6 GCCcore/10.2.0 4.6 GCCcore/10.3.0 4.8 GCCcore/11.2.0 4.8 GCCcore/11.3.0 4.8.1 GCCcore/12.2.0 4.8.1 GCCcore/12.3.0 4.8.2 GCCcore/12.2.0 4.8.2 GCCcore/13.2.0 4.8.2 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/Cufflinks/","title":"Cufflinks","text":"Transcript assembly, differential expression, and differential regulation for RNA-Seq
homepage: http://cole-trapnell-lab.github.io/cufflinks/
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","boost":0.5},{"location":"version-specific/supported-software/c/Cython/","title":"Cython","text":"The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.
homepage: https://pypi.python.org/pypi/Cython/
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","boost":0.5},{"location":"version-specific/supported-software/c/Cytoscape/","title":"Cytoscape","text":"Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.
homepage: https://cytoscape.org/
version versionsuffix toolchain 3.9.1 -Java-11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/c-ares/","title":"c-ares","text":"c-ares is a C library for asynchronous DNS requests (including name resolves)
homepage: https://c-ares.haxx.se
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","boost":0.5},{"location":"version-specific/supported-software/c/cDNA_Cupcake/","title":"cDNA_Cupcake","text":"cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.
homepage: https://github.com/Magdoll/cDNA_Cupcake
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","boost":0.5},{"location":"version-specific/supported-software/c/cURL/","title":"cURL","text":"libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.
homepage: http://curl.haxx.se
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","boost":0.5},{"location":"version-specific/supported-software/c/cadaver/","title":"cadaver","text":"cadaver is a command-line WebDAV client for Unix.
homepage: http://www.webdav.org/cadaver/
version toolchain 0.23.3 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cairo/","title":"cairo","text":"Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB
homepage: http://cairographics.org
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","boost":0.5},{"location":"version-specific/supported-software/c/cairomm/","title":"cairomm","text":"The Cairomm package provides a C++ interface to Cairo.
homepage: http://cairographics.org
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","boost":0.5},{"location":"version-specific/supported-software/c/canu/","title":"canu","text":"Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II or Oxford Nanopore MinION). Canu is a hierarchical assembly pipeline which runs in four steps: Detect overlaps in high-noise sequences using MHAP Generate corrected sequence consensus Trim corrected sequences Assemble trimmed corrected sequences
homepage: https://github.com/marbl/canu
version versionsuffix toolchain 1.4 foss/2016b 1.7 intel/2018a 1.8 -Perl-5.28.1 GCCcore/8.2.0 1.8 -Perl-5.26.0 foss/2017b 1.8 -Perl-5.28.0 foss/2018b 1.8 -Perl-5.26.0 intel/2017b 1.9 -Java-11 GCCcore/8.3.0 2.1.1 GCCcore/10.2.0 2.1.1 -Java-11 GCCcore/9.3.0 2.2 GCC/12.2.0 2.2 -Java-11 GCCcore/10.3.0 2.2 GCCcore/10.3.0 2.2 GCCcore/11.2.0 2.2 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/captum/","title":"captum","text":"Captum is a model interpretability and understanding library for PyTorch. Captum means comprehension in Latin and contains general purpose implementations of integrated gradients, saliency maps, smoothgrad, vargrad and others for PyTorch models. It has quick integration for models built with domain-specific libraries such as torchvision, torchtext, and others.
homepage: https://captum.ai/
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","boost":0.5},{"location":"version-specific/supported-software/c/carputils/","title":"carputils","text":"carputils is a Python framework for generating and running openCARP examples.
homepage: https://git.opencarp.org/openCARP/carputils
version versionsuffix toolchain 20200915 -Python-3.8.2 foss/2020a 20210513 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/casacore/","title":"casacore","text":"A suite of C++ libraries for radio astronomy data processing. The ephemerides data needs to be in DATA_DIR and the location must be specified at runtime. Thus user's can update them.
homepage: https://github.com/casacore/casacore
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","boost":0.5},{"location":"version-specific/supported-software/c/castor/","title":"castor","text":"Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format.
homepage: https://CRAN.R-project.org/package=castor
version toolchain 1.7.11 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/category_encoders/","title":"category_encoders","text":"A set of scikit-learn-style transformers for encoding categorical variables into numeric by means of different techniques.
homepage: https://github.com/scikit-learn-contrib/category_encoders
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","boost":0.5},{"location":"version-specific/supported-software/c/causallift/","title":"causallift","text":"CausalLift: Python package for Uplift Modeling in real-world business; applicable for both A/B testing and observational data
homepage: https://github.com/Minyus/causallift
version versionsuffix toolchain 1.0.6 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/causalml/","title":"causalml","text":"Causal ML: A Python Package for Uplift Modeling and Causal Inference with ML
homepage: https://github.com/uber/causalml
version versionsuffix toolchain 0.3.0-20180610 -Python-3.7.2 foss/2019a 0.8.0-20200909 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/ccache/","title":"ccache","text":"ccache-3.1.9: Cache for C/C++ compilers
homepage: http://ccache.samba.org/
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","boost":0.5},{"location":"version-specific/supported-software/c/cclib/","title":"cclib","text":"cclib is a Python library that provides parsers for computational chemistry log files. It alsoprovides a platform to implement algorithms in a package-independent manner.
homepage: http://cclib.github.io/
version versionsuffix toolchain 1.5 -Python-3.5.2 foss/2016b 1.6.3 -Python-3.8.2 foss/2020a 1.6.3 -Python-3.8.2 intel/2020a 1.7.2 foss/2021b 1.8 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cctbx-base/","title":"cctbx-base","text":"The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix project. The goal of the Phenix project is to advance automation of macromolecular structure determination. Phenix depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific applications.
homepage: https://github.com/cctbx/cctbx_project
version toolchain 2020.8 foss/2020b 2020.8 fosscuda/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cctools/","title":"cctools","text":"The Cooperating Computing Tools (CCTools) help you to design and deploy scalable applications that run on hundreds or thousands of machines at once.
homepage: https://ccl.cse.nd.edu/
version toolchain 7.0.22 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cdbfasta/","title":"cdbfasta","text":"Fasta file indexing and retrival tool
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version toolchain 0.99 GCC/8.3.0 0.99 iccifort/2019.1.144-GCC-8.2.0-2.31.1 0.99 iccifort/2019.5.281 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cddlib/","title":"cddlib","text":"An efficient implementation of the Double Description Method
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","boost":0.5},{"location":"version-specific/supported-software/c/cdo-bindings/","title":"cdo-bindings","text":"Python interface to CDO.
homepage: https://github.com/Try2Code/cdo-bindings
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","boost":0.5},{"location":"version-specific/supported-software/c/cell2location/","title":"cell2location","text":"Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
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","boost":0.5},{"location":"version-specific/supported-software/c/centerline/","title":"centerline","text":"Roads, rivers and similar linear structures are often represented by long and complex polygons. Since one of the most important attributes of a linear structure is its length, extracting that attribute from a polygon can prove to be more or less difficult. This library tries to solve this problem by creating the the polygon's centerline using the Voronoi diagram. For more info on how to use this package, see the official documentation.
homepage: https://github.com/fitodic/centerline
version toolchain 1.0.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cffi/","title":"cffi","text":"C Foreign Function Interface for Python. Interact with almost any C code from Python, based on C-like declarations that you can often copy-paste from header files or documentation.
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","boost":0.5},{"location":"version-specific/supported-software/c/cfgrib/","title":"cfgrib","text":"A Python interface to map GRIB files to the NetCDF Common Data Model following the CF Convention using ecCodes.
homepage: https://github.com/ecmwf/cfgrib/
version toolchain 0.9.14.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cftime/","title":"cftime","text":"Time-handling functionality from netcdf4-python
homepage: https://github.com/Unidata/cftime
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","boost":0.5},{"location":"version-specific/supported-software/c/cget/","title":"cget","text":"Cmake package retrieval. This can be used to download and install cmake packages
homepage: https://cget.readthedocs.io/en/latest/index.html
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","boost":0.5},{"location":"version-specific/supported-software/c/charm-gems/","title":"charm-gems","text":"This repository contains the gems C++ code and python bindings used in Freesurfer's Sequence-Adaptive Multimodal SEGmentation (SAMSEG) and in SimNIBS 4.0 Complete Head Anatomy Reconstruction Method (CHARM) to create individualized head models for electric field simulations.
homepage: https://github.com/simnibs/charm-gems
version toolchain 1.3.3 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/chemprop/","title":"chemprop","text":"Message Passing Neural Networks for Molecule Property Prediction
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","boost":0.5},{"location":"version-specific/supported-software/c/chewBBACA/","title":"chewBBACA","text":"chewBBACA stands for \"BSR-Based Allele Calling Algorithm\". chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci.
homepage: https://github.com/B-UMMI/chewBBACA
version versionsuffix toolchain 2.5.5 -Python-3.8.2 intel/2020a 3.3.9 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/chi2comb/","title":"chi2comb","text":"Cumulative density function of linear combinations of independent chi-square random variables and a standard Normal distribution. As of now, this is basically a repackaging of the davies function implemented in the CompQuadForm library for R.
homepage: https://github.com/limix/chi2comb
version toolchain 0.0.3 GCCcore/7.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/chopper/","title":"chopper","text":"Rust implementation of NanoFilt+NanoLyse, both originally written in Python. This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file. Filtering is done on average read quality and minimal or maximal read length, and applying a headcrop (start of read) and tailcrop (end of read) while printing the reads passing the filter.
homepage: https://github.com/wdecoster/chopper
version toolchain 0.9.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/chromVARmotifs/","title":"chromVARmotifs","text":"The goal of chromVARmotifs is to make it easy to use several different motif collections in R, particularly for use with motifmatchr and chromVAR packages.
homepage: https://github.com/GreenleafLab/chromVARmotifs
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","boost":0.5},{"location":"version-specific/supported-software/c/cicero/","title":"cicero","text":"Cicero is an R package that provides tools for analyzing single-cell chromatin accessibility experiments.
homepage: https://cole-trapnell-lab.github.io/cicero-release
version versionsuffix toolchain 1.3.4.11 -R-4.0.3-Monocle3 foss/2020b 1.3.8 -R-4.2.1-Monocle3 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cimfomfa/","title":"cimfomfa","text":"This library supports both MCL, a cluster algorithm for graphs, and zoem, a macro/DSL language. It supplies abstractions for memory management, I/O, associative arrays, strings, heaps, and a few other things. The string library has had heavy testing as part of zoem. Both understandably and regrettably I chose long ago to make it C-string-compatible, hence nul bytes may not be part of a string. At some point I hope to rectify this, perhaps unrealistically.
homepage: https://github.com/micans/cimfomfa
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","boost":0.5},{"location":"version-specific/supported-software/c/cisTEM/","title":"cisTEM","text":"cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
homepage: https://cistem.org/
version toolchain 1.0.0-beta foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cliquer/","title":"cliquer","text":"Cliquer is a set of C routines for finding cliques in an arbitrary weighted graph. It uses an exact branch-and-bound algorithm developed by Patric Ostergard. It is designed with the aim of being efficient while still being flexible and easy to use.
homepage: https://users.aalto.fi/~pat/cliquer.html
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","boost":0.5},{"location":"version-specific/supported-software/c/cmocean/","title":"cmocean","text":"This package contains colormaps for commonly-used oceanographic variables. Most of the colormaps started from matplotlib colormaps, but have now been adjusted using the viscm tool to be perceptually uniform.
homepage: https://github.com/matplotlib/cmocean
version toolchain 2.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cmph/","title":"cmph","text":"Cmph is a free minimal perfect hash C library, providing several algorithms in the literature in a consistent, ease to use, API.
homepage: https://sourceforge.net/projects/cmph/
version toolchain 2.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/code-cli/","title":"code-cli","text":"Visual Studio Code is a lightweight but powerful source code editor which runs on your desktop and is available for Windows, macOS and Linux. It comes with built-in support for JavaScript, TypeScript and Node.js and has a rich ecosystem of extensions for other languages and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin your journey with VS Code with these introductory videos.
homepage: https://code.visualstudio.com/
version versionsuffix toolchain 1.85.1 -x64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/code-server/","title":"code-server","text":"Run VS Code on any machine anywhere and access it in the browser.
homepage: https://github.com/cdr/code-server
version toolchain 3.7.3 system 4.16.1 system 4.21.1 system 4.22.1 system 4.89.1 system 4.9.1 system 4.90.2 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/colorize/","title":"colorize","text":"Ruby gem for colorizing text using ANSI escape sequences. Extends String class or add a ColorizedString with methods to set the text color, background color and text effects.
homepage: https://github.com/fazibear/colorize
version toolchain 0.7.7 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/colossalai/","title":"colossalai","text":"Colossal-AI: A Unified Deep Learning System for Big Model Era
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version versionsuffix toolchain 0.1.8 -CUDA-11.3.1 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/conan/","title":"conan","text":"Decentralized, open-source (MIT), C/C++ package manager.
homepage: https://conan.io
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","boost":0.5},{"location":"version-specific/supported-software/c/configparser/","title":"configparser","text":"configparser is a Python library that brings the updated configparser from Python 3.5 to Python 2.6-3.5
homepage: https://docs.python.org/3/library/configparser.html
version versionsuffix toolchain 3.5.0 -Python-2.7.11 foss/2016a 3.5.0 -Python-2.7.12 foss/2016b 3.5.0 -Python-2.7.12 intel/2016b 3.5.0 -Python-3.5.2 intel/2016b 3.5.0 -Python-3.6.3 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/configurable-http-proxy/","title":"configurable-http-proxy","text":"HTTP proxy for node.js including a REST API for updating the routing table. Developed as a part of the Jupyter Hub multi-user server.
homepage: https://github.com/jupyterhub/configurable-http-proxy
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","boost":0.5},{"location":"version-specific/supported-software/c/connected-components-3d/","title":"connected-components-3d","text":"cc3d is an implementation of connected components in three dimensions using a 26, 18, or 6-connected neighborhood in 3D or 4 and 8-connected in 2D.
homepage: https://github.com/seung-lab/connected-components-3d/
version toolchain 3.12.1 foss/2022b 3.14.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/contextily/","title":"contextily","text":"contextily is a small Python 3 package to retrieve tile maps from the internet. It can add those tiles as basemap to matplotlib figures or write tile maps to disk into geospatial raster files. Bounding boxes can be passed in both WGS84 (EPSG:4326) and Spheric Mercator (EPSG:3857).
homepage: https://contextily.readthedocs.io/
version toolchain 1.5.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cooler/","title":"cooler","text":"Cooler is a support library for a storage format, also called cooler, used to store genomic interaction data of any size, such as Hi-C contact matrices.
homepage: https://open2c.github.io/cooler
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","boost":0.5},{"location":"version-specific/supported-software/c/core-counter/","title":"core-counter","text":"Tool to check available cores and OMP threads
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","boost":0.5},{"location":"version-specific/supported-software/c/corner/","title":"corner","text":"Make some beautiful corner plots.
homepage: https://corner.readthedocs.io/en/latest/
version versionsuffix toolchain 2.0.1 -Python-2.7.15 foss/2019a 2.0.1 -Python-3.7.2 foss/2019a 2.2.2 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/coverage/","title":"coverage","text":"Coverage.py is a tool for measuring code coverage of Python programs. It monitors your program, noting which parts of the code have been executed, then analyzes the source to identify code that could have been executed but was not.
homepage: https://coverage.readthedocs.io
version versionsuffix toolchain 4.5.1 -Python-2.7.14 intel/2017b 5.5 GCCcore/10.2.0 5.5 GCCcore/10.3.0 7.2.3 GCCcore/12.2.0 7.2.3 GCCcore/12.3.0 7.2.7 GCCcore/11.3.0 7.4.4 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cowsay/","title":"cowsay","text":"Configurable talking characters in ASCII art
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version toolchain 3.04 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/coxeter/","title":"coxeter","text":"A library for the study of combinatorial aspects of Coxeter group theory
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version toolchain 20180226 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cpio/","title":"cpio","text":"The cpio package contains tools for archiving.
homepage: https://savannah.gnu.org/projects/cpio/
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","boost":0.5},{"location":"version-specific/supported-software/c/cppy/","title":"cppy","text":"A small C++ header library which makes it easier to write Python extension modules. The primary feature is a PyObject smart pointer which automatically handles reference counting and provides convenience methods for performing common object operations.
homepage: https://github.com/nucleic/cppy
version toolchain 1.1.0 GCCcore/10.3.0 1.1.0 GCCcore/11.2.0 1.2.1 GCCcore/11.3.0 1.2.1 GCCcore/12.2.0 1.2.1 GCCcore/12.3.0 1.2.1 GCCcore/13.2.0 1.2.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cppyy/","title":"cppyy","text":"cppyy is an automatic, run-time, Python-C++ bindings generator, for calling C++ from Python and Python from C++.
homepage: https://cppyy.readthedocs.io
version toolchain 3.0.0 GCCcore/11.3.0 3.1.2 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cppzmq/","title":"cppzmq","text":"cppzmq is a C++ binding for libzmq.
homepage: https://github.com/zeromq/cppzmq
version toolchain 4.9.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cpu_features/","title":"cpu_features","text":"A cross-platform C library to retrieve CPU features (such as available instructions) at runtime.
homepage: https://github.com/google/cpu_features
version toolchain 0.6.0 GCCcore/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cram/","title":"cram","text":"Cram is a functional testing framework for command line applications.
homepage: https://bitheap.org/cram
version toolchain 0.7 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cramino/","title":"cramino","text":"A tool for quick quality assessment of cram and bam files, intended for long read sequencing.
homepage: https://github.com/wdecoster/cramino
version toolchain 0.14.5 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cramtools/","title":"cramtools","text":"CRAMTools is a set of Java tools and APIs for efficient compression of sequence read data. Although this is intended as a stable version the code is released as early access. Parts of the CRAMTools are experimental and may not be supported in the future.
homepage: https://github.com/enasequence/cramtools/
version versionsuffix toolchain 2.0 -Java-1.7.0_80 system 3.0 -Java-1.7.0_80 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/crb-blast/","title":"crb-blast","text":"Conditional Reciprocal Best BLAST - high confidence ortholog assignment.
homepage: https://github.com/cboursnell/crb-blast
version versionsuffix toolchain 0.6.9 GCC/12.3.0 0.6.9 -Ruby-2.6.1 foss/2018b 0.6.9 gompi/2021a 0.6.9 gompi/2021b 0.6.9 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cromwell/","title":"cromwell","text":"Cromwell is a Workflow Management System geared towards scientific workflows.
homepage: http://cromwell.readthedocs.io/
version versionsuffix toolchain 56 -Java-11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/crossguid/","title":"crossguid","text":"CrossGuid is a minimal, cross platform, C++ GUID library. It uses the best native GUID/UUID generator on the given platform and has a generic class for parsing, stringifying, and comparing IDs. The guid generation technique is determined by your platform:
homepage: https://github.com/graeme-hill/crossguid
version toolchain 20190529 GCCcore/11.2.0 20190529 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cryoCARE/","title":"cryoCARE","text":"This package is a memory efficient implementation of cryoCARE. This setup trains a denoising U-Net for tomographic reconstruction according to the Noise2Noise training paradigm. Therefore the user has to provide two tomograms of the same sample. The simplest way to achieve this is with direct- detector movie-frames. You can use Warp to generate two reconstructed tomograms based on the even/odd frames. Alternatively, the movie-frames can be split in two halves (e.g. with MotionCor2 -SplitSum 1 or with IMOD alignframes -debug 10000) from which two identical, up to random noise, tomograms can be reconstructed. These two (even and odd) tomograms can be used as input to this cryoCARE implementation.
homepage: https://github.com/juglab/cryoCARE_pip
version versionsuffix toolchain 0.2.1 -CUDA-11.3.1 foss/2021a 0.3.0 -CUDA-11.7.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cryoDRGN/","title":"cryoDRGN","text":"cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous reconstruction. CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.
homepage: https://cb.csail.mit.edu/cb/cryodrgn/
version versionsuffix toolchain 0.3.2 fosscuda/2020b 0.3.5 -CUDA-11.3.1 foss/2021a 1.0.0-beta -CUDA-11.3.1 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/crypt4gh/","title":"crypt4gh","text":"crypt4gh is a Python tool to encrypt, decrypt or re-encrypt files, according to the GA4GH encryption file format.
homepage: https://github.com/EGA-archive/crypt4gh
version toolchain 1.7 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cryptography/","title":"cryptography","text":"cryptography is a package designed to expose cryptographic primitives and recipes to Python developers.
homepage: https://github.com/pyca/cryptography
version toolchain 41.0.1 GCCcore/12.3.0 41.0.5 GCCcore/13.2.0 42.0.8 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cscope/","title":"cscope","text":"Cscope is a developer's tool for browsing source code.
homepage: http://cscope.sourceforge.net/
version toolchain 15.9 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/csvkit/","title":"csvkit","text":"csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats.
homepage: https://github.com/wireservice/csvkit
version versionsuffix toolchain 1.0.4 GCCcore/8.2.0 1.0.5 -Python-3.7.4 GCCcore/8.3.0 1.1.0 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/ctags/","title":"ctags","text":"Ctags generates an index (or tag) file of language objects found in source files that allows these items to be quickly and easily located by a text editor or other utility.
homepage: http://ctags.sourceforge.net/
version toolchain 5.8 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/ctffind/","title":"ctffind","text":"Program for finding CTFs of electron micrographs.
homepage: https://grigoriefflab.umassmed.edu/ctffind4
version versionsuffix toolchain 4.1.13 foss/2019a 4.1.13 fosscuda/2019a 4.1.13 fosscuda/2019b 4.1.14 foss/2019b 4.1.14 -CUDA-11.3.1 foss/2021a 4.1.14 foss/2021b 4.1.14 foss/2022a 4.1.14 foss/2022b 4.1.14 foss/2023a 4.1.14 fosscuda/2019b 4.1.14 fosscuda/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/ctffind5/","title":"ctffind5","text":"Program for finding CTFs of electron micrographs.
homepage: https://grigoriefflab.umassmed.edu/ctf_estimation_ctffind_ctftilt
version toolchain 5.0.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cuDNN/","title":"cuDNN","text":"The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
homepage: https://developer.nvidia.com/cudnn
version versionsuffix toolchain 4.0 system 5.0 -CUDA-7.5.18 system 5.0-rc system 5.1 -CUDA-8.0.44 system 6.0 -CUDA-8.0.61 system 6.0.21 -CUDA-7.5.18 system 6.0.21 -CUDA-8.0.44 system 7.0.2 -CUDA-9.0.176 system 7.0.5 -CUDA-8.0.44 system 7.0.5 -CUDA-9.0.176 system 7.0.5 -CUDA-9.1.85 system 7.0.5.15 fosscuda/2017b 7.0.5.15 fosscuda/2018a 7.0.5.15 intelcuda/2017b 7.1.4.18 fosscuda/2018b 7.4.2.24 -CUDA-10.0.130 system 7.4.2.24 gcccuda/2019a 7.5.0.56 -CUDA-10.0.130 system 7.6.2.24 -CUDA-10.1.243 system 7.6.4.38 -CUDA-10.0.130 system 7.6.4.38 gcccuda/2019a 7.6.4.38 gcccuda/2019b 8.0.4.30 -CUDA-11.0.2 system 8.0.4.30 -CUDA-11.1.1 system 8.0.5.39 -CUDA-11.1.1 system 8.1.0.77 -CUDA-11.2.1 system 8.1.1.33 -CUDA-11.2.1 system 8.2.1.32 -CUDA-11.3.1 system 8.2.2.26 -CUDA-11.4.0 system 8.2.2.26 -CUDA-11.4.1 system 8.4.0.27 -CUDA-11.6.0 system 8.4.1.50 -CUDA-11.5.2 system 8.4.1.50 -CUDA-11.6.0 system 8.4.1.50 -CUDA-11.7.0 system 8.5.0.96 -CUDA-11.7.0 system 8.6.0.163 -CUDA-11.8.0 system 8.7.0.84 -CUDA-11.8.0 system 8.8.0.121 -CUDA-12.0.0 system 8.9.2.26 -CUDA-12.1.1 system 8.9.2.26 -CUDA-12.2.0 system 8.9.7.29 -CUDA-12.3.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cuSPARSELt/","title":"cuSPARSELt","text":"NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix
homepage: https://docs.nvidia.com/cuda/cusparselt/index.html
version versionsuffix toolchain 0.3.0.3 -CUDA-11.4.1 system 0.6.0.6 -CUDA-12.1.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cuTENSOR/","title":"cuTENSOR","text":"The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, reduction and elementwise operations.
homepage: https://developer.nvidia.com/cutensor
version versionsuffix toolchain 1.2.2.5 -CUDA-11.1.1 system 1.2.2.5 gcccuda/2019b 1.6.0.3 -CUDA-11.3.1 system 1.6.1.5 -CUDA-11.4.1 system 1.6.1.5 -CUDA-11.7.0 system 1.7.0.1 -CUDA-12.0.0 system 2.0.1.2 -CUDA-12.1.1 system 2.0.1.2 -CUDA-12.2.2 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/currentNe/","title":"currentNe","text":"Estimation of current effective population using artificial neural networks.
homepage: https://github.com/esrud/currentNe
version toolchain 1.0.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/custodian/","title":"custodian","text":"A simple JIT job management framework in Python.
homepage: https://pypi.python.org/pypi/custodian
version versionsuffix toolchain 1.1.0 -Python-2.7.13 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cutadapt/","title":"cutadapt","text":"Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
homepage: https://opensource.scilifelab.se/projects/cutadapt/
version versionsuffix toolchain 1.14 -Python-2.7.13 foss/2017a 1.14 -Python-2.7.13 intel/2017a 1.15 -Python-3.5.2 foss/2016b 1.16 -Python-2.7.14 foss/2017b 1.16 -Python-3.6.3 foss/2017b 1.16 -Python-3.6.4 foss/2018a 1.16 -Python-2.7.14 intel/2017b 1.16 -Python-3.6.3 intel/2017b 1.16 -Python-2.7.14 intel/2018a 1.16 -Python-3.6.4 intel/2018a 1.18 -Python-2.7.18 GCC/10.2.0 1.18 GCCcore/8.2.0 1.18 GCCcore/8.3.0 1.18 -Python-2.7.15 foss/2018b 1.18 -Python-3.6.6 foss/2018b 1.18 -Python-3.6.6 intel/2018b 1.9.1 -Python-2.7.11 foss/2016a 1.9.1 -Python-2.7.12 foss/2016b 2.1 -Python-3.6.6 foss/2018b 2.10 GCCcore/10.2.0 2.10 -Python-3.7.4 GCCcore/8.3.0 2.10 -Python-3.8.2 GCCcore/9.3.0 2.7 -Python-3.7.4 GCCcore/8.3.0 2.8 -Python-3.7.4 GCCcore/8.3.0 3.4 GCCcore/10.2.0 3.4 GCCcore/10.3.0 3.5 GCCcore/11.2.0 4.2 GCCcore/11.3.0 4.4 GCCcore/12.2.0 4.9 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cuteSV/","title":"cuteSV","text":"cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection.
homepage: https://github.com/tjiangHIT/cuteSV
version toolchain 2.0.3 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cwltool/","title":"cwltool","text":"Common workflow language (CWL) reference implementation.
homepage: https://github.com/common-workflow-language/cwltool
version toolchain 3.1.20221008225030 foss/2021a 3.1.20221018083734 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cxxopts/","title":"cxxopts","text":"cxxopts is a lightweight C++ command line option parser
homepage: https://github.com/jarro2783/cxxopts
version toolchain 3.0.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cysignals/","title":"cysignals","text":"The cysignals package provides mechanisms to handle interrupts (and other signals and errors) in Cython code.
homepage: https://pypi.org/project/cysignals/
version versionsuffix toolchain 1.10.2 -Python-2.7.14 foss/2017b 1.10.2 -Python-3.6.3 foss/2017b 1.10.2 -Python-2.7.14 intel/2017b 1.10.2 -Python-3.6.3 intel/2017b 1.11.2 GCCcore/11.3.0 1.11.4 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cython-blis/","title":"cython-blis","text":"Fast BLAS-like operations from Python and Cython, without the tears. Provides the Blis linear algebra routines as a self-contained Python C-extension.
homepage: https://github.com/explosion/cython-blis
version toolchain 0.9.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cytoolz/","title":"cytoolz","text":"Cython implementation of the toolz package, which provides high performance utility functions for iterables, functions, and dictionaries.
homepage: https://github.com/pytoolz/cytoolz
version versionsuffix toolchain 0.10.1 -Python-3.7.2 GCCcore/8.2.0 0.10.1 -Python-3.6.6 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cytosim/","title":"cytosim","text":"Cytosim is a cytoskeleton simulation engine written in C++ working on Mac OS, GNU/Linux and Windows (with Cygwin).
homepage: https://github.com/nedelec/cytosim
version versionsuffix toolchain 20190117 -mkl gomkl/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/c/cyvcf2/","title":"cyvcf2","text":"cython + htslib == fast VCF and BCF processing
homepage: https://github.com/brentp/cyvcf2
version versionsuffix toolchain 0.10.10 -Python-3.6.6 foss/2018b 0.11.5 foss/2019a 0.11.5 intel/2019a 0.31.1 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/","title":"List of supported software (d)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- dadi
- dagitty
- Dakota
- DALI
- DaliLite
- Dalton
- damageproto
- dammit
- DANPOS2
- DAS_Tool
- dask
- dask-labextension
- datalad
- datamash
- davix
- DB
- DB_File
- DBCSR
- DBD-mysql
- DBG2OLC
- dblatex
- DBus
- dbus-glib
- dclone
- dcm2niix
- DCMTK
- dd
- deal.II
- deap
- decona
- deconf
- DeconICA
- deepdiff
- deepfold
- DeepLabCut
- DeepLoc
- deepmedic
- DeepMod2
- DeepSurv
- deepTools
- DEICODE
- Delft3D
- Delly
- DeltaLake
- DeMixT
- Demystify
- DendroPy
- denseweight
- DensPart
- Deprecated
- desktop-file-utils
- destiny
- Detectron2
- DETONATE
- devbio-napari
- Devito
- DFA
- DFT-D3
- DFT-D4
- DFTB+
- dftd3-lib
- dftd4
- DGL
- DIA-NN
- DIAL
- dialog
- DIALOGUE
- DIAMOND
- Dice
- DiCE-ML
- dicom2nifti
- DicomBrowser
- dictys
- DiffBind
- Diffutils
- dijitso
- dill
- DIRAC
- distributed
- DistributedStream
- DjVuLibre
- DL_POLY_4
- DL_POLY_Classic
- DL_POLY_Classic_GUI
- dlb
- dlib
- DLPack
- dm-haiku
- dm-reverb
- dm-tree
- DMCfun
- DMLC-Core
- DMTCP
- DOLFIN
- dominate
- dorado
- Doris
- DosageConvertor
- dotNET-Core
- dotNET-Core-Runtime
- dotNET-SDK
- double-conversion
- DoubletFinder
- Doxygen
- DP3
- DRAGMAP
- Drake
- dRep
- drmaa-python
- DROP
- dropEst
- DSA
- dSFMT
- DSRC
- Dsuite
- dtcmp
- dtcwt
- DualSPHysics
- dub
- DUBStepR
- dune-core
- dune-fem
- duplex-tools
- dx-toolkit
- dxpy
- DyMat
- dynesty
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/DALI/","title":"DALI","text":"R-package for the analysis of single-cell TCR/BCR data in the Seurat ecosystem
homepage: https://github.com/vibscc/DALI
version versionsuffix toolchain 2.1.2 -R-4.2.2 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/DANPOS2/","title":"DANPOS2","text":"A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2
homepage: https://sites.google.com/site/danposdoc
version versionsuffix toolchain 2.2.2 -Python-2.7.12 foss/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/DAS_Tool/","title":"DAS_Tool","text":"DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
homepage: https://github.com/cmks/DAS_Tool
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","boost":0.5},{"location":"version-specific/supported-software/d/DB/","title":"DB","text":"Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
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","boost":0.5},{"location":"version-specific/supported-software/d/DBCSR/","title":"DBCSR","text":"DBCSR stands for Distributed Blocked Compressed Sparse Row. DBCSR is a library designed to efficiently perform sparse matrix-matrix multiplication, among other operations.
homepage: https://cp2k.github.io/dbcsr/develop/
version toolchain 2.5.0 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/DBD-mysql/","title":"DBD-mysql","text":"Perl binding for MySQL
homepage: http://search.cpan.org/~capttofu/DBD-mysql-4.032/
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","boost":0.5},{"location":"version-specific/supported-software/d/DBG2OLC/","title":"DBG2OLC","text":"DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies
homepage: https://github.com/yechengxi/DBG2OLC
version toolchain 20170208 intel/2016b 20170208 intel/2017a 20180221 GCC/6.4.0-2.28 20180221 iccifort/2017.4.196-GCC-6.4.0-2.28 20200724 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/DB_File/","title":"DB_File","text":"Perl5 access to Berkeley DB version 1.x.
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","boost":0.5},{"location":"version-specific/supported-software/d/DBus/","title":"DBus","text":"D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a \"single instance\" application or daemon, and to launch applications and daemons on demand when their services are needed.
homepage: http://dbus.freedesktop.org/doc/dbus-glib
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","boost":0.5},{"location":"version-specific/supported-software/d/DCMTK/","title":"DCMTK","text":"DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers.
homepage: https://dicom.offis.de/dcmtk
version toolchain 3.6.3 GCCcore/7.3.0 3.6.5 GCCcore/8.2.0 3.6.5 GCCcore/8.3.0 3.6.6 GCCcore/10.3.0 3.6.6 GCCcore/11.2.0 3.6.7 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/DEICODE/","title":"DEICODE","text":"DEICODE is a form of Aitchison Distance that is robust to high levels of sparsity. DEICODE utilizes a natural solution to the zero problem formulated in recommendation systems called matrix completion. A simple way to interpret the method is, as a robust compositional PCA (via SVD) where zero values do not influence the resulting ordination.
homepage: https://library.qiime2.org/plugins/deicode/19/
version toolchain 0.2.4 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/DETONATE/","title":"DETONATE","text":"DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.
homepage: http://deweylab.biostat.wisc.edu/detonate/
version toolchain 1.11 GCC/12.3.0 1.11 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/DFA/","title":"DFA","text":"Python library for modeling DFAs, Moore Machines, and Transition Systems.
homepage: https://github.com/mvcisback/dfa
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","boost":0.5},{"location":"version-specific/supported-software/d/DFT-D3/","title":"DFT-D3","text":"DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.
homepage: https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3
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","boost":0.5},{"location":"version-specific/supported-software/d/DFT-D4/","title":"DFT-D4","text":"Generally Applicable Atomic-Charge Dependent London Dispersion Correction.
homepage: https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dftd4
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","boost":0.5},{"location":"version-specific/supported-software/d/DFTB%2B/","title":"DFTB+","text":"DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of magnitude in speed.
homepage: https://www.dftb-plus.info
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","boost":0.5},{"location":"version-specific/supported-software/d/DGL/","title":"DGL","text":"DGL is an easy-to-use, high performance and scalable Python package for deep learning on graphs. DGL is framework agnostic, meaning if a deep graph model is a component of an end-to-end application, the rest of the logics can be implemented in any major frameworks, such as PyTorch, Apache MXNet or TensorFlow.
homepage: https://www.dgl.ai
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","boost":0.5},{"location":"version-specific/supported-software/d/DIA-NN/","title":"DIA-NN","text":"DIA-NN is a universal software for data-independent acquisition (DIA) proteomics data processing.
homepage: https://github.com/vdemichev/DiaNN
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","boost":0.5},{"location":"version-specific/supported-software/d/DIAL/","title":"DIAL","text":"DIAL (De novo Identification of Alleles) is a collection of programs to automate the discovery of alleles for a species where we lack a reference sequence. The SNPs/alleles are specifically selected for a low error rate in genotyping assays.
homepage: http://www.bx.psu.edu/miller_lab/
version toolchain 2011.06.06 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/DIALOGUE/","title":"DIALOGUE","text":"DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.
homepage: https://github.com/livnatje/DIALOGUE
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","boost":0.5},{"location":"version-specific/supported-software/d/DIAMOND/","title":"DIAMOND","text":"Accelerated BLAST compatible local sequence aligner
homepage: https://github.com/bbuchfink/diamond
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","boost":0.5},{"location":"version-specific/supported-software/d/DIRAC/","title":"DIRAC","text":"DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations
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","boost":0.5},{"location":"version-specific/supported-software/d/DLPack/","title":"DLPack","text":"DLPack is a stable in-memory data structure for an ndarray system to interact with a variety of frameworks.
homepage: https://dmlc.github.io/dlpack/latest/
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","boost":0.5},{"location":"version-specific/supported-software/d/DL_POLY_4/","title":"DL_POLY_4","text":"DL_POLY is a general purpose classical molecular dynamics (MD) simulation software
homepage: https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx
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","boost":0.5},{"location":"version-specific/supported-software/d/DL_POLY_Classic/","title":"DL_POLY_Classic","text":"DL_POLY Classic is a general purpose (parallel and serial) molecular dynamics simulation package.
homepage: https://gitlab.com/DL_POLY_Classic/dl_poly
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","boost":0.5},{"location":"version-specific/supported-software/d/DL_POLY_Classic_GUI/","title":"DL_POLY_Classic_GUI","text":"The DL_POLY Graphical User Interface (or GUI) is a program written in the Java language and is intended for use with the DL_POLY molecular simulation program. This is the GUI for DL_POLY Classic, it can also be used for DL_POLY_4.
homepage: https://gitlab.com/DL_POLY_Classic/dl_poly
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","boost":0.5},{"location":"version-specific/supported-software/d/DMLC-Core/","title":"DMLC-Core","text":"DMLC-Core is the backbone library to support all DMLC projects, offers the bricks to build efficient and scalable distributed machine learning libraries.
homepage: https://dmlc-core.readthedocs.io/en/latest
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","boost":0.5},{"location":"version-specific/supported-software/d/DMTCP/","title":"DMTCP","text":"DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space -- with no modifications to user code or to the O/S.
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","boost":0.5},{"location":"version-specific/supported-software/d/DOLFIN/","title":"DOLFIN","text":"DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations.
homepage: https://bitbucket.org/fenics-project/dolfin
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","boost":0.5},{"location":"version-specific/supported-software/d/DP3/","title":"DP3","text":"DP3: streaming processing pipeline for radio interferometric data.
homepage: https://dp3.readthedocs.io/
version toolchain 6.0 foss/2022a 6.0 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/DRAGMAP/","title":"DRAGMAP","text":"Dragmap is the Dragen mapper/aligner Open Source Software.
homepage: https://github.com/Illumina/DRAGMAP
version toolchain 1.3.0 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/DROP/","title":"DROP","text":"Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
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","boost":0.5},{"location":"version-specific/supported-software/d/DSA/","title":"DSA","text":"Digital Sorting Algorithm
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","boost":0.5},{"location":"version-specific/supported-software/d/DSRC/","title":"DSRC","text":"DNA Sequence Reads Compression is an application designed for compression of data files containing reads from DNA sequencing in FASTQ format. The amount of such files can be huge, e.g., a few (or tens) of gigabytes, so a need for a robust data compression tool is clear. Usually universal compression programs like gzip or bzip2 are used for this purpose, but it is obvious that a specialized tool can work better.
homepage: http://sun.aei.polsl.pl/dsrc
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","boost":0.5},{"location":"version-specific/supported-software/d/DUBStepR/","title":"DUBStepR","text":"DUBStepR (Determining the Underlying Basis using Step-wise Regression) is a feature selection algorithm for cell type identification in single-cell RNA-sequencing data.
homepage: https://github.com/prabhakarlab/DUBStepR
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","boost":0.5},{"location":"version-specific/supported-software/d/Dakota/","title":"Dakota","text":"The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models.
homepage: https://dakota.sandia.gov/
version toolchain 6.16.0 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/DaliLite/","title":"DaliLite","text":"DaliLite is a light version of the software run by the Dali server. The web server has search and data visualization options which are not included in this package. DaliLite supports data import (import.pl) to convert PDB entries to Dali's internal data format and pairwise comparison (dali.pl) to structurally align a list of query structures to a list of target structures.
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version toolchain 4.1 gompi/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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","boost":0.5},{"location":"version-specific/supported-software/d/datamash/","title":"datamash","text":"GNU datamash performs basic numeric, textual and statistical operations on input data files
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","boost":0.5},{"location":"version-specific/supported-software/d/davix/","title":"davix","text":"The davix project aims to make file management over HTTP-based protocols simple. The focus is on high-performance remote I/O and data management of large collections of files. Currently, there is support for the WebDav (link is external), Amazon S3 (link is external), Microsoft Azure (link is external), and HTTP (link is external) protocols.
homepage: https://dmc.web.cern.ch/projects/davix/home
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","boost":0.5},{"location":"version-specific/supported-software/d/dblatex/","title":"dblatex","text":"dblatex is a program that transforms your SGML/XML DocBook documents to DVI, PostScript or PDF by translating them into pure LaTeX as a first process. MathML 2.0 markups are supported, too. It started as a clone of DB2LaTeX.
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","boost":0.5},{"location":"version-specific/supported-software/d/dclone/","title":"dclone","text":"Low level functions for implementing maximum likelihood estimating procedures for complex models using data cloning and Bayesian Markov chain Monte Carlo methods
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","boost":0.5},{"location":"version-specific/supported-software/d/dcm2niix/","title":"dcm2niix","text":"dcm2niix is a designed program to convert neuroimaging data from the DICOM format to the NIfTI format.
homepage: https://github.com/rordenlab/dcm2niix
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homepage: https://github.com/tulip-control/dd
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","boost":0.5},{"location":"version-specific/supported-software/d/deal.II/","title":"deal.II","text":"deal.II is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements.
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homepage: http://deap.readthedocs.org/en/master/
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homepage: http://deeptools.readthedocs.org/
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homepage: https://deepdiff.readthedocs.io/en/latest/
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homepage: https://github.com/steimi/denseweight
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homepage: https://github.com/haesleinhuepf/devbio-napari
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","boost":0.5},{"location":"version-specific/supported-software/d/dijitso/","title":"dijitso","text":"dijitso is a Python module for distributed just-in-time shared library building.
homepage: https://bitbucket.org/fenics-project/dijitso
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","boost":0.5},{"location":"version-specific/supported-software/d/dill/","title":"dill","text":"dill extends python's pickle module for serializing and de-serializing python objects to the majority of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse of which is converting a byte stream back to on python object hierarchy.
homepage: https://pypi.org/project/dill/
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","boost":0.5},{"location":"version-specific/supported-software/d/dlb/","title":"dlb","text":"DLB is a dynamic library designed to speed up HPC hybrid applications (i.e., two levels of parallelism) by improving the load balance of the outer level of parallelism (e.g., MPI) by dynamically redistributing the computational resources at the inner level of parallelism (e.g., OpenMP). at run time.
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","boost":0.5},{"location":"version-specific/supported-software/d/dlib/","title":"dlib","text":"Dlib is a modern C++ toolkit containing machine learning algorithms and tools for creating complex software in C++ to solve real world problems. It is used in both industry and academia in a wide range of domains including robotics, embedded devices, mobile phones, and large high performance computing environments.
homepage: https://github.com/davisking/dlib
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homepage: https://github.com/deepmind/dm-haiku
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","boost":0.5},{"location":"version-specific/supported-software/d/dm-reverb/","title":"dm-reverb","text":"Reverb is an efficient and easy-to-use data storage and transport system designed for machine learning research. Reverb is primarily used as an experience replay system for distributed reinforcement learning algorithms but the system also supports multiple data structure representations such as FIFO, LIFO, and priority queues.
homepage: https://github.com/deepmind/reverb
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","boost":0.5},{"location":"version-specific/supported-software/d/dm-tree/","title":"dm-tree","text":"dm-tree provides tree, a library for working with nested data structures. In a way, tree generalizes the builtin map function which only supports flat sequences, and allows to apply a function to each \"leaf\" preserving the overall structure.
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homepage: https://github.com/Knio/dominate/
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","boost":0.5},{"location":"version-specific/supported-software/d/dotNET-Core/","title":"dotNET-Core","text":".NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Contains the SDK and the Runtime.
homepage: https://www.microsoft.com/net/
version toolchain 6.0.420 system 6.0 system 8.0.203 system 8.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/dotNET-SDK/","title":"dotNET-SDK","text":".NET is a free, cross-platform, open source developer platform for building many different types of applications.
homepage: https://www.microsoft.com/net/
version versionsuffix toolchain 3.1.300 -linux-x64 system 6.0.101 -linux-x64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/double-conversion/","title":"double-conversion","text":"Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.
homepage: https://github.com/google/double-conversion
version toolchain 3.0.3 foss/2018a 3.1.4 GCCcore/8.2.0 3.1.4 GCCcore/8.3.0 3.1.5 GCCcore/10.2.0 3.1.5 GCCcore/10.3.0 3.1.5 GCCcore/11.2.0 3.1.5 GCCcore/9.3.0 3.2.0 GCCcore/11.3.0 3.2.1 GCCcore/12.2.0 3.3.0 GCCcore/12.3.0 3.3.0 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/drmaa-python/","title":"drmaa-python","text":"Distributed Resource Management Application API (DRMAA) bindings for Python.
homepage: https://github.com/pygridtools/drmaa-python
version versionsuffix toolchain 0.7.9 -slurm GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/dropEst/","title":"dropEst","text":"Pipeline for initial analysis of droplet-based single-cell RNA-seq data
homepage: https://github.com/hms-dbmi/dropEst
version versionsuffix toolchain 0.7.1 -R-3.4.3 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/dtcmp/","title":"dtcmp","text":"Datatype Compare (DTCMP) Library for sorting and ranking distributed data using MPI
homepage: https://github.com/llnl/dtcmp
version toolchain 1.1.0 gompi/2019a 1.1.0 gompi/2020a 1.1.0 iimpi/2019a 1.1.0 iimpi/2020a 1.1.2 gompi/2020b 1.1.4 gompi/2022a 1.1.4 gompi/2023a 1.1.5 gompi/2024a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/dtcwt/","title":"dtcwt","text":"Dual-Tree Complex Wavelet Transform library for Python
homepage: https://github.com/rjw57/dtcwt
version versionsuffix toolchain 0.12.0 -Python-2.7.15 foss/2018b 0.12.0 -Python-3.7.4 intel/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/dub/","title":"dub","text":"Package and build manager for D applications and libraries
homepage: https://github.com/dlang/dub
version toolchain 1.38.1 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/dune-core/","title":"dune-core","text":"The Dune core modules build the stable basis of Dune. They follow a consistent release cycle and have high requirements regarding stability and backwards compatibility. These modules build the foundation for higher-level components.
homepage: https://www.dune-project.org/groups/core/
version toolchain 2.8.0.post1 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/dune-fem/","title":"dune-fem","text":"DUNE-FEM is a discretization module based on DUNE containing all the building blocks required to implement efficient solvers for a wide range of (systems of non linear) partial differential equations. DUNE-FEM can also be used through an extensive Python interface which brings all components of DUNE-FEM and the DUNE core modules to Python.
homepage: https://www.dune-project.org/modules/dune-fem/
version toolchain 2.8.0.6 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/duplex-tools/","title":"duplex-tools","text":"Duplex Tools contains a set of utilities for dealing with Duplex sequencing data. Tools are provided to identify and prepare duplex pairs for basecalling by Dorado (recommended) and Guppy, and for recovering simplex basecalls from incorrectly concatenated pairs.
homepage: https://github.com/nanoporetech/duplex-tools
version toolchain 0.3.1 foss/2022a 0.3.3 foss/2022a 0.3.3 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/dx-toolkit/","title":"dx-toolkit","text":"The DNAnexus Platform SDK - also called dx-toolkit - includes the dx command-line client; tools for building and debugging apps; utilities for working with DNA data on the DNAnexus Platform; and Python, Java, C++ and R bindings for working on the DNAnexus Platform.
homepage: https://documentation.dnanexus.com/downloads#dnanexus-platform-sdk
version toolchain 0.350.1 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/dxpy/","title":"dxpy","text":"DNAnexus Platform API bindings for Python
homepage: http://autodoc.dnanexus.com/
version versionsuffix toolchain 0.266.1 -Python-2.7.14 intel/2018a 0.345.0 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/d/dynesty/","title":"dynesty","text":"dynesty is a Pure Python, MIT-licensed Dynamic Nested Sampling package for estimating Bayesian posteriors and evidences.
homepage: https://dynesty.readthedocs.io/
version toolchain 2.1.3 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/","title":"List of supported software (e)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- E-ANTIC
- e3nn
- ea-utils
- earthengine-api
- easel
- EasyBuild
- EasyMocap
- EasyQC
- ebGSEA
- ecBuild
- ecCodes
- eccodes-python
- ecFlow
- ECL
- eclib
- ED2
- EDirect
- edlib
- EGA-QuickView
- EggLib
- eggnog-mapper
- EGTtools
- eht-imaging
- Eigen
- EigenExa
- EIGENSOFT
- einops
- elastix
- elbencho
- ELFIO
- elfutils
- Elk
- Elmer
- ELPA
- ELPH
- elprep
- ELSI
- ELSI-RCI
- Emacs
- EMAN2
- EMBOSS
- Embree
- emcee
- EMMAX
- empanada-dl
- empanada-napari
- EMU
- enaBrowserTool
- enchant
- enchant-2
- EnergyPlus
- EnsEMBLCoreAPI
- ensmallen
- entrypoints
- epct
- EPD
- EPIC
- epiScanpy
- EpiSCORE
- eQuilibrator
- EricScript
- ESIpy
- ESL-Bundle
- ESM-2
- ESM3
- ESMF
- ESMPy
- ESMValTool
- eSpeak-NG
- ESPResSo
- Essentia
- ETE
- ETSF_IO
- eudev
- EUKulele
- EVcouplings
- Evcxr-REPL
- EveryBeam
- EvidentialGene
- evince
- evmix
- ExaBayes
- ExaML
- Excel-Writer-XLSX
- ExifTool
- exiv2
- Exonerate
- expat
- expect
- expecttest
- eXpress
- ExpressBetaDiversity
- Extrae
- ExtremeLy
- EZC3D
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/E-ANTIC/","title":"E-ANTIC","text":"E-ANTIC is a C/C++ library to deal with real embedded number fields built on top of ANTIC (https://github.com/wbhart/antic). Its aim is to have as fast as possible exact arithmetic operations and comparisons.
homepage: https://github.com/videlec/e-antic
version toolchain 0.1.2 GCC/8.2.0-2.31.1 0.1.5 GCC/8.3.0 1.3.0 gfbf/2022a 2.0.2 gfbf/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/ECL/","title":"ECL","text":"ECL (Embeddable Common-Lisp) is an interpreter of the Common-Lisp language as described in the X3J13 Ansi specification, featuring CLOS (Common-Lisp Object System), conditions, loops, etc, plus a translator to C, which can produce standalone executables.
homepage: https://ecl.common-lisp.dev/
version toolchain 23.9.9 GCCcore/11.3.0 24.5.10 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/ED2/","title":"ED2","text":"The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry
homepage: https://github.com/EDmodel/ED2
version versionsuffix toolchain 20170201 -serial intel/2017a 20170201 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/EDirect/","title":"EDirect","text":"Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases from a Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in a variety of formats.
homepage: https://www.ncbi.nlm.nih.gov/books/NBK25501/
version toolchain 19.7.20230531 GCCcore/10.3.0 20.5.20231006 GCCcore/12.2.0 20.5.20231006 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/EGA-QuickView/","title":"EGA-QuickView","text":"EGA-QuickView is a FUSE file system to access EGA files remotely.
homepage: https://github.com/EGA-archive/ega-quickview
version toolchain 20240620 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/EGTtools/","title":"EGTtools","text":"EGTtools provides a centralized repository with analytical and numerical methods to study/model game theoretical problems under the Evolutionary Game Theory (EGT) framework.
homepage: https://github.com/Socrats/EGTTools
version toolchain 0.1.10.dev2 foss/2021b 0.1.11 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/EIGENSOFT/","title":"EIGENSOFT","text":"The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker\u2019s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.
homepage: http://www.hsph.harvard.edu/alkes-price/software/
version toolchain 6.0.1 foss/2016a 6.1.1 foss/2016a 6.1.4 foss/2016b 7.2.1 foss/2018b 7.2.1 foss/2019a 7.2.1 foss/2019b 7.2.1 foss/2020b 7.2.1 foss/2021a 7.2.1 intel/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/ELFIO/","title":"ELFIO","text":"ELFIO is a header-only C++ library intended for reading and generating files in the ELF binary format.
homepage: http://elfio.sourceforge.net
version toolchain 3.9 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/ELPA/","title":"ELPA","text":"Eigenvalue SoLvers for Petaflop-Applications .
homepage: http://elpa.mpcdf.mpg.de
version versionsuffix toolchain 2015.02.002 foss/2018a 2015.02.002 gimkl/2017a 2015.02.002 intel/2018a 2016.05.004 intel/2016b 2016.05.004 intel/2017a 2016.11.001.pre foss/2018b 2016.11.001.pre intel/2018b 2017.11.001 foss/2018b 2017.11.001 intel/2018a 2017.11.001 intel/2018b 2018.05.001 foss/2018b 2018.05.001 intel/2018b 2018.11.001 intel/2019a 2019.11.001 foss/2019b 2019.11.001 foss/2020a 2019.11.001 intel/2019b 2019.11.001 intel/2020a 2019.11.001 iomkl/2019b 2020.05.001 intel/2020a 2020.11.001 foss/2020b 2020.11.001 intel/2020b 2021.05.001 foss/2021a 2021.05.001 foss/2021b 2021.05.001 intel/2021a 2021.05.001 intel/2021b 2021.05.002 intel/2020b 2021.11.001 foss/2021b 2021.11.001 foss/2022a 2021.11.001 intel/2021b 2021.11.001 intel/2022a 2021.11.001 intel/2022b 2022.05.001 -CUDA-11.7.0 foss/2022a 2022.05.001 foss/2022a 2022.05.001 -CUDA-12.0.0 foss/2022b 2022.05.001 foss/2022b 2022.05.001 intel/2022a 2022.05.001 intel/2022b 2023.05.001 foss/2023a 2023.05.001 intel/2023a 2023.11.001 foss/2023b 2023.11.001 intel/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/ELPH/","title":"ELPH","text":"ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. We have used ELPH to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs).
homepage: http://ccb.jhu.edu/software/ELPH/index.shtml
version toolchain 1.0.1 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/ELSI-RCI/","title":"ELSI-RCI","text":"ELSI-RCI provides and enhances open-source software packages which iteratively solve or circumvent eigenvalue problems in self-consistent field calculations based on the Kohn-Sham density-functional theory.
homepage: https://wordpress.elsi-interchange.org/
version toolchain 0.1.0 GCC/10.3.0 0.1.0 GCC/11.2.0 0.1.0 foss/2020b 0.1.0 intel/2020b 0.1.0 intel-compilers/2021.2.0 0.1.0 intel-compilers/2021.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/ELSI/","title":"ELSI","text":"ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. The ELSI infrastructure should also be useful for other challenging eigenvalue problems.
homepage: https://wordpress.elsi-interchange.org/
version versionsuffix toolchain 2.11.0 -PEXSI foss/2023a 2.5.0 -PEXSI foss/2019b 2.5.0 foss/2019b 2.5.0 -PEXSI intel/2019b 2.5.0 intel/2019b 2.6.4 -PEXSI foss/2020b 2.6.4 -PEXSI intel/2020b 2.7.1 -PEXSI foss/2021a 2.7.1 -PEXSI intel/2021a 2.9.1 -PEXSI foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/EMAN2/","title":"EMAN2","text":"EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.
homepage: http://blake.bcm.edu/emanwiki/EMAN2
version versionsuffix toolchain 2.21a -Python-2.7.14-Boost-1.63.0 foss/2018a 2.3 -Python-2.7.15 foss/2019a 2.3 -Python-2.7.15 fosscuda/2019a 2.3 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/EMBOSS/","title":"EMBOSS","text":"EMBOSS is 'The European Molecular Biology Open Software Suite' . EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
homepage: https://emboss.sourceforge.net/
version versionsuffix toolchain 6.6.0 -Java-13 GCC/10.2.0 6.6.0 GCC/8.2.0-2.31.1 6.6.0 -Java-11 GCC/8.3.0 6.6.0 foss/2016b 6.6.0 foss/2018b 6.6.0 foss/2021a 6.6.0 foss/2021b 6.6.0 iccifort/2019.1.144-GCC-8.2.0-2.31.1 6.6.0 -X11-20170314 intel/2017a 6.6.0 intel/2017a 6.6.0 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/EMMAX/","title":"EMMAX","text":"EMMAX is a statistical test for large scale human or model organism association mapping accounting for the sample structure
homepage: https://csg.sph.umich.edu//kang/emmax
version toolchain 20100310 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/EMU/","title":"EMU","text":"EMU infers population structure in the presence of missingness and works for both haploid, psuedo-haploid and diploid genotype datasets
homepage: http://www.popgen.dk/software/index.php/EMU
version versionsuffix toolchain 0.66 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/EPD/","title":"EPD","text":"The Enthought Python Distribution provides scientists with a comprehensive set of tools to perform rigorous data analysis and visualization. Python, distinguished by its flexibility, coherence, and ease-of-use, is rapidly becoming the programming language of choice for researchers worldwide. EPD extends this capacity with a powerful collection of Python libraries to enable interactive technical computing and cross-platform rapid application development.
homepage: http://www.enthought.com/products/edudownload.php
version toolchain 7.3-2-rh5 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/EPIC/","title":"EPIC","text":"Package implementing EPIC method to estimate the proportion of immune, stromal, endothelial and cancer or other cells from bulk gene expression data.
homepage: https://gfellerlab.shinyapps.io/EPIC_1-1
version versionsuffix toolchain 1.1 -R-3.5.1 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/ESIpy/","title":"ESIpy","text":"Program aimed at the calculation of population analysis and aromaticity indicators from different Hilbert space partitions.
homepage: https://github.com/jgrebol/ESIpy
version toolchain 20240709 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/ESL-Bundle/","title":"ESL-Bundle","text":"The ESL Bundle is a collection of libraries and utilities broadly used in electronic structure calculations, put together to make their use easier by researchers and scientific software developers. ESL stands for Electronic Structure Library, an initiative which distributes quality software and promotes open standards for high-performance computing applications in the field of electronic structure calculations.
homepage: https://esl.cecam.org
version toolchain 0.6.1 foss/2020b 0.6.1 intel/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/ESM-2/","title":"ESM-2","text":"ESM-2 outperforms all tested single-sequence protein language models across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate accurate structure predictions end to end directly from the sequence of a protein.
homepage: https://github.com/facebookresearch/esm
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","boost":0.5},{"location":"version-specific/supported-software/e/ESM3/","title":"ESM3","text":"ESM3 is a frontier generative model for biology, able to jointly reason across three fundamental biological properties of proteins: sequence, structure, and function. These three data modalities are represented as tracks of discrete tokens at the input and output of ESM3. You can present the model with a combination of partial inputs across the tracks, and ESM3 will provide output predictions for all the tracks.
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","boost":0.5},{"location":"version-specific/supported-software/e/ESMF/","title":"ESMF","text":"The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models.
homepage: http://sourceforge.net/projects/esmf
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","boost":0.5},{"location":"version-specific/supported-software/e/ESMPy/","title":"ESMPy","text":"Earth System Modeling Framework (ESMF) Python Interface
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","boost":0.5},{"location":"version-specific/supported-software/e/ESMValTool/","title":"ESMValTool","text":"The Earth System Model eValuation Tool (ESMValTool) is a community diagnostics and performance metrics tool for the evaluation of Earth System Models (ESMs) that allows for routine comparison of single or multiple models, either against predecessor versions or against observations.
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","boost":0.5},{"location":"version-specific/supported-software/e/ESPResSo/","title":"ESPResSo","text":"A software package for performing and analyzing scientific Molecular Dynamics simulations.
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","boost":0.5},{"location":"version-specific/supported-software/e/ETSF_IO/","title":"ETSF_IO","text":"A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL.
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version toolchain 2.0.6 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 0.1.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 1.5.2 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://easybuilders.github.io/easybuild
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homepage: https://chingswy.github.io/easymocap-public-doc/
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","boost":0.5},{"location":"version-specific/supported-software/e/EasyQC/","title":"EasyQC","text":"EasyQC is an R-package that provides advanced functionality to (1) perform file-level QC of single genome-wide association (GWA) data-sets (2) conduct quality control across several GWA data-sets (meta-level QC) (3) simplify data-handling of large-scale GWA data-sets.
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","boost":0.5},{"location":"version-specific/supported-software/e/EggLib/","title":"EggLib","text":"EggLib is a C++/Python library and program package for evolutionary genetics and genomics.
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","boost":0.5},{"location":"version-specific/supported-software/e/Eigen/","title":"Eigen","text":"Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
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","boost":0.5},{"location":"version-specific/supported-software/e/EigenExa/","title":"EigenExa","text":"EigenExa, a part of KMATHLIB, is a high performance eigen-solver.
homepage: https://www.r-ccs.riken.jp/labs/lpnctrt/projects/eigenexa/
version toolchain 2.11 intel/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/Elk/","title":"Elk","text":"An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universit\u00e4t Graz as a milestone of the EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably.
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version toolchain 4.0.15 intel/2016b 4.3.6 intel/2017a 6.3.2 intel/2019b 7.0.12 foss/2020b 7.2.42 foss/2021a 8.5.2 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 9.0 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/Emacs/","title":"Emacs","text":"GNU Emacs is an extensible, customizable text editor\u2014and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing.
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","boost":0.5},{"location":"version-specific/supported-software/e/EvidentialGene/","title":"EvidentialGene","text":"EvidentialGene is a genome informatics project for \"Evidence Directed Gene Construction for Eukaryotes\", for constructing high quality, accurate gene sets for animals and plants (any eukaryotes), being developed by Don Gilbert at Indiana University, gilbertd at indiana edu.
homepage: http://arthropods.eugenes.org/EvidentialGene/
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","boost":0.5},{"location":"version-specific/supported-software/e/Excel-Writer-XLSX/","title":"Excel-Writer-XLSX","text":"The Excel::Writer::XLSX module can be used to create an Excel file in the 2007+ XLSX format. Multiple worksheets can be added to a workbook and formatting can be applied to cells. Text, numbers, and formulas can be written to the cells.
homepage: https://metacpan.org/pod/Excel::Writer::XLSX
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version toolchain 12.00 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/Exonerate/","title":"Exonerate","text":"Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
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","boost":0.5},{"location":"version-specific/supported-software/e/Extrae/","title":"Extrae","text":"Extrae is the core instrumentation package developed by the Performance Tools group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered by Extrae typically includes timestamped events of runtime calls, performance counters and source code references. Besides, Extrae provides its own API to allow the user to manually instrument his or her application.
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version toolchain 2.3.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/e3nn/","title":"e3nn","text":"Euclidean neural networks (e3nn) is a python library based on pytorch to create equivariant neural networks for the group O(3).
homepage: https://e3nn.org/
version versionsuffix toolchain 0.3.3 -CUDA-11.7.0 foss/2022a 0.3.3 -PyTorch-1.13.1-CUDA-11.7.0 foss/2022a 0.3.3 foss/2022a 0.3.3 -CUDA-12.1.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/eQuilibrator/","title":"eQuilibrator","text":"Calculation of standard thermodynamic potentials of biochemical reactions.
homepage: https://equilibrator.weizmann.ac.il/
version toolchain 0.4.7 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/eSpeak-NG/","title":"eSpeak-NG","text":"The eSpeak NG is a compact open source software text-to-speech synthesizer for Linux, Windows, Android and other operating systems. It supports more than 100 languages and accents. It is based on the eSpeak engine created by Jonathan Duddington.
homepage: https://github.com/espeak-ng/espeak-ng
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","boost":0.5},{"location":"version-specific/supported-software/e/eXpress/","title":"eXpress","text":"Streaming quantification for high-throughput sequencing
homepage: https://pachterlab.github.io/eXpress
version toolchain 1.5.1 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/ea-utils/","title":"ea-utils","text":"Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.
homepage: http://expressionanalysis.github.io/ea-utils/
version toolchain 1.04.807 foss/2016a 1.04.807 foss/2016b 1.04.807 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/earthengine-api/","title":"earthengine-api","text":"Python and JavaScript bindings for calling the Earth Engine API
homepage: https://github.com/google/earthengine-api
version versionsuffix toolchain 0.1.143 -Python-2.7.14 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/easel/","title":"easel","text":"Easel supports computational analysis of biological sequences using probabilistic models.
homepage: https://bioeasel.org/
version toolchain 0.48 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/ebGSEA/","title":"ebGSEA","text":"Gene Set Enrichment Analysis is one of the most common tasks in the analysis of omic data, and is critical for biological interpretation. In the context of Epigenome Wide Association Studies (EWAS), which typically rank individual cytosines according to the level of differential methylation, enrichment analysis of biological pathways is challenging due to differences in CpG/probe density between genes.
homepage: https://github.com/aet21/ebGSEA
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","boost":0.5},{"location":"version-specific/supported-software/e/ecBuild/","title":"ecBuild","text":"A CMake-based build system, consisting of a collection of CMake macros and functions that ease the managing of software build systems
homepage: https://ecbuild.readthedocs.io/
version toolchain 3.7.0 system 3.8.0 system 3.8.5 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/ecCodes/","title":"ecCodes","text":"ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).
homepage: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home
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","boost":0.5},{"location":"version-specific/supported-software/e/ecFlow/","title":"ecFlow","text":"ecFlow is a client/server workflow package that enables users to run a large number of programs (with dependencies on each other and on time) in a controlled environment. It provides reasonable tolerance for hardware and software failures, combined with restart capabilities. It is used at ECMWF to run all our operational suites across a range of platforms.
homepage: https://ecflow.readthedocs.io/en/latest/index.html
version toolchain 5.7.0 GCC/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/eccodes-python/","title":"eccodes-python","text":"Python 3 interface to decode and encode GRIB and BUFR files via the ECMWF ecCodes library.
homepage: https://github.com/ecmwf/eccodes-python
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","boost":0.5},{"location":"version-specific/supported-software/e/eclib/","title":"eclib","text":"The eclib package includes mwrank (for 2-descent on elliptic curves over Q) and modular symbol code used to create the elliptic curve database.
homepage: https://github.com/JohnCremona/eclib
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","boost":0.5},{"location":"version-specific/supported-software/e/edlib/","title":"edlib","text":"Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.
homepage: https://martinsos.github.io/edlib
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","boost":0.5},{"location":"version-specific/supported-software/e/eggnog-mapper/","title":"eggnog-mapper","text":"eggnog-mapper is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments
homepage: http://eggnog-mapper.embl.de
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","boost":0.5},{"location":"version-specific/supported-software/e/eht-imaging/","title":"eht-imaging","text":"Python modules for simulating and manipulating VLBI data and producing images with regularized maximum likelihood methods.
homepage: https://github.com/achael/eht-imaging
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","boost":0.5},{"location":"version-specific/supported-software/e/einops/","title":"einops","text":"Flexible and powerful tensor operations for readable and reliable code. Supports numpy, pytorch, tensorflow, jax, and others.
homepage: https://einops.rocks/
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","boost":0.5},{"location":"version-specific/supported-software/e/elastix/","title":"elastix","text":"elastix: a toolbox for rigid and nonrigid registration of images.
homepage: http://elastix.isi.uu.nl/
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","boost":0.5},{"location":"version-specific/supported-software/e/elbencho/","title":"elbencho","text":"A distributed storage benchmark for files, objects & blocks with support for GPUs
homepage: https://github.com/breuner/elbencho
version toolchain 2.0-3 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/elfutils/","title":"elfutils","text":"The elfutils project provides libraries and tools for ELF files and DWARF data.
homepage: https://elfutils.org/
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","boost":0.5},{"location":"version-specific/supported-software/e/elprep/","title":"elprep","text":"elPrep is a high-performance tool for analyzing .sam/.bam files (up to and including variant calling) in sequencing pipelines.
homepage: https://github.com/ExaScience/elprep
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","boost":0.5},{"location":"version-specific/supported-software/e/emcee/","title":"emcee","text":"Emcee is an extensible, pure-Python implementation of Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. It's designed for Bayesian parameter estimation and it's really sweet!
homepage: https://dfm.io/emcee
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","boost":0.5},{"location":"version-specific/supported-software/e/empanada-dl/","title":"empanada-dl","text":"Tool for panoptic segmentation of organelles in 2D and 3D electron microscopy (EM) images.
homepage: https://empanada.readthedocs.io/
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","boost":0.5},{"location":"version-specific/supported-software/e/empanada-napari/","title":"empanada-napari","text":"Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari.
homepage: https://empanada.readthedocs.io/
version toolchain 1.1.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/enaBrowserTool/","title":"enaBrowserTool","text":"enaBrowserTools is a set of scripts that interface with the ENA web services to download data from ENA easily, without any knowledge of scripting required.
homepage: https://github.com/enasequence/enaBrowserTools/
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","boost":0.5},{"location":"version-specific/supported-software/e/enchant-2/","title":"enchant-2","text":"Enchant aims to provide a simple but comprehensive abstraction for dealing with different spell checking libraries in a consistent way. A client, such as a text editor or word processor, need not know anything about a specific spell-checker, and since all back-ends are plugins, new spell-checkers can be added without needing any change to the program using Enchant.
homepage: https://github.com/AbiWord/enchant
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","boost":0.5},{"location":"version-specific/supported-software/e/enchant/","title":"enchant","text":"Enchant is a library (and command-line program) that wraps a number of different spelling libraries and programs with a consistent interface.
homepage: https://abiword.github.io/enchant/
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","boost":0.5},{"location":"version-specific/supported-software/e/ensmallen/","title":"ensmallen","text":"ensmallen is a high-quality C++ library for non-linear numerical optimization
homepage: https://ensmallen.org/
version toolchain 2.21.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/entrypoints/","title":"entrypoints","text":"Entry points are a way for Python packages to advertise objects with some common interface.
homepage: https://github.com/takluyver/entrypoints
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","boost":0.5},{"location":"version-specific/supported-software/e/epct/","title":"epct","text":"This is the epct (EUMETSAT Product Customisation Toolbox) Python package for the EUMETSAT Data Tailor. The EUMETSAT Data Tailor makes it possible for users to subset and aggregate EUMETSAT data products in space and time, filter layers, generate quicklooks, project onto new coordinate reference systems, and reformat into common GIS formats (netCDF, GeoTIFF, etc.).
homepage: https://gitlab.eumetsat.int/eumetlab/data-services/eumdac
version toolchain 3.2.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/epiScanpy/","title":"epiScanpy","text":"EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq analysis tool Scanpy (Genome Biology, 2018) [Wolf18].
homepage: https://github.com/colomemaria/episcanpy
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","boost":0.5},{"location":"version-specific/supported-software/e/eudev/","title":"eudev","text":"eudev is a fork of systemd-udev with the goal of obtaining better compatibility with existing software such as OpenRC and Upstart, older kernels, various toolchains and anything else required by users and various distributions.
homepage: https://wiki.gentoo.org/wiki/Project:Eudev
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","boost":0.5},{"location":"version-specific/supported-software/e/evince/","title":"evince","text":"Evince is a document viewer for multiple document formats. The goal of evince is to replace the multiple document viewers that exist on the GNOME Desktop with a single simple application.
homepage: https://wiki.gnome.org/Apps/Evince
version toolchain 45.0 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/e/evmix/","title":"evmix","text":"evmix: Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corrected Kernel Density Estimation
homepage: https://cran.r-project.org/web/packages/evmix
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","boost":0.5},{"location":"version-specific/supported-software/e/exiv2/","title":"exiv2","text":"Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata.
homepage: https://exiv2.org
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","boost":0.5},{"location":"version-specific/supported-software/e/expat/","title":"expat","text":"Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)
homepage: https://libexpat.github.io
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","boost":0.5},{"location":"version-specific/supported-software/e/expect/","title":"expect","text":"Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. Expect really makes this stuff trivial. Expect is also useful for testing these same applications.
homepage: https://core.tcl.tk/expect/index
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","boost":0.5},{"location":"version-specific/supported-software/e/expecttest/","title":"expecttest","text":"This library implements expect tests (also known as \"golden\" tests). Expect tests are a method of writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and the test framework automatically populates the expected output. If the output of the test changes, you can rerun the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.
homepage: https://github.com/ezyang/expecttest
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","boost":0.5},{"location":"version-specific/supported-software/f/","title":"List of supported software (f)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- f90cache
- f90nml
- f90wrap
- Faber
- FabIO
- FACE
- faceswap
- Faiss
- FALCON
- FANN
- fast5
- FASTA
- fasta-reader
- fastahack
- fastai
- FastaIndex
- FastANI
- Fastaq
- fastfilters
- FastFold
- fastjet
- fastjet-contrib
- FastME
- fastml
- fastp
- fastparquet
- fastPHASE
- fastq-pair
- fastq-tools
- FastQ_Screen
- FastQC
- fastqsplitter
- FastQTL
- fastqz
- FastRFS
- fastStructure
- FastTree
- FastViromeExplorer
- FASTX-Toolkit
- fatslim
- fbm
- FBPIC
- FCM
- fdict
- FDMNES
- FDS
- fdstools
- FDTD_Solutions
- feh
- FEniCS
- fermi-lite
- Ferret
- festival
- fetchMG
- FFAVES
- FFC
- FFLAS-FFPACK
- FFmpeg
- ffnet
- ffnvcodec
- fftlib
- FFTW
- FFTW.MPI
- fgbio
- FGSL
- FHI-aims
- FIAT
- FIGARO
- FigureGen
- Fiji
- file
- filevercmp
- Filtlong
- find_circ
- finder
- findhap
- findutils
- fineRADstructure
- fineSTRUCTURE
- fio
- Fiona
- Firefox
- FIRESTARTER
- FireWorks
- fish
- FIt-SNE
- FIX
- fixesproto
- FLAC
- FLAIR
- flair-NLP
- FLANN
- FLASH
- flash-attention
- Flask
- flatbuffers
- flatbuffers-python
- Flax
- FLEUR
- flex
- Flexbar
- FlexiBLAS
- FlexiDot
- Flink
- FLINT
- flit
- flook
- flowFDA
- FLTK
- FLUENT
- Flye
- FMILibrary
- FMM3D
- FMPy
- FMRIprep
- FMS
- fmt
- FoBiS
- FoldX
- fontconfig
- fontsproto
- fonttools
- forbear
- FORD
- foss
- fosscuda
- FoX
- FOX-Toolkit
- fplll
- FPM
- fpocket
- fpylll
- fqtrim
- fqzcomp
- FragGeneScan
- FragPipe
- FRANz
- FreeBarcodes
- freebayes
- FreeFEM
- FreeFem++
- freeglut
- FreeImage
- FreeSASA
- FreeSurfer
- FreeTDS
- freetype
- freetype-py
- FreeXL
- freud-analysis
- FriBidi
- FRUIT
- FRUIT_processor
- FSL
- FSLeyes
- fsm-lite
- fsom
- FSON
- ftfy
- FTGL
- fugue
- fullrmc
- fumi_tools
- funannotate
- FunGAP
- FUNWAVE-TVD
- FUSE
- FuSeq
- FusionCatcher
- futhark
- futile
- future
- fxtract
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FACE/","title":"FACE","text":"A Fortran Ansi Colors (and Styles) Environment. A KISS pure Fortran Library for easy colorize (and stylize) strings.
homepage: https://github.com/szaghi/FACE
version toolchain 1.1.1 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FALCON/","title":"FALCON","text":"Falcon: a set of tools for fast aligning long reads for consensus and assembly
homepage: https://github.com/PacificBiosciences/FALCON
version versionsuffix toolchain 1.8.8 intel/2017b 1.8.8 -Python-2.7.16 intel/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FANN/","title":"FANN","text":"Fast Artificial Neural Network Library is a free open source neural network library, which implements multilayer artificial neural networks in C with support for both fully connected and sparsely connected networks.
homepage: http://leenissen.dk
version toolchain 2.2.0 GCCcore/6.4.0 2.2.0 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FASTA/","title":"FASTA","text":"The FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.
homepage: http://fasta.bioch.virginia.edu
version toolchain 36.3.5e foss/2016b 36.3.8i GCC/11.2.0 36.3.8i GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FASTX-Toolkit/","title":"FASTX-Toolkit","text":"The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
homepage: http://hannonlab.cshl.edu/fastx_toolkit/
version toolchain 0.0.14 GCC/10.3.0 0.0.14 GCC/11.2.0 0.0.14 GCC/11.3.0 0.0.14 GCC/9.3.0 0.0.14 GCCcore/7.3.0 0.0.14 foss/2016a 0.0.14 foss/2016b 0.0.14 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FBPIC/","title":"FBPIC","text":"FBPIC (Fourier-Bessel Particle-In-Cell) is a Particle-In-Cell (PIC) code for relativistic plasma physics. It is especially well-suited for physical simulations of laser-wakefield acceleration and plasma-wakefield acceleration.
homepage: https://fbpic.github.io/
version toolchain 0.20.3 fosscuda/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FCM/","title":"FCM","text":"FCM is a set of tools for managing and building source code.
homepage: http://www.metoffice.gov.uk/research/collaboration/fcm
version toolchain 2.3.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FDMNES/","title":"FDMNES","text":"X-ray spectroscopies are techniques which probe the electronic and structural properties of the materials. Most often performed at synchrotron, they are extensively used to analyse all classes of materials. The advances on the experimental side need the complementary progress on the theoretical side to extract confidentely all the information the data can furnish. In this context, the purpose of our FDMNES project is to supply to the community a user friendly ab initio code to simulate X-ray absorption and emission spectroscopies as well as resonant x-ray scattering and x-ray Raman spectroscopies, among other techniques. FDMNES, for Finite Difference Method Near Edge Structure, uses the density functional theory (DFT). It is thus specially devoted to the simulation of the K edges of all the chemical elements and of the L23 edges of the heavy ones. For the other edges, it includes advances by the use of the time dependent DFT (TD-DFT).
homepage: https://fdmnes.neel.cnrs.fr
version toolchain 2024-02-29 gomkl/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FDS/","title":"FDS","text":"Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires.
homepage: https://code.google.com/p/fds-smv/
version versionsuffix toolchain 6.0.1 -no-OFED system 6.5.2 intel/2016b 6.5.3 intel/2017a 6.6.0 intel/2017b 6.6.0 intel/2018a 6.7.0 intel/2018a 6.7.4 intel/2020a 6.7.5 intel/2020a 6.7.6 intel/2020b 6.7.7 intel/2021b 6.7.9 intel/2022a 6.8.0 intel/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FDTD_Solutions/","title":"FDTD_Solutions","text":"High performance FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials.
homepage: http://www.lumerical.com/tcad-products/fdtd/
version toolchain 8.11.337 system 8.16.982 system 8.20.1731 system 8.6.2 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FEniCS/","title":"FEniCS","text":"FEniCS is a computing platform for solving partial differential equations (PDEs).
homepage: https://fenicsproject.org/
version versionsuffix toolchain 2019.1.0 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FFAVES/","title":"FFAVES","text":"Functional Feature Amplification Via Entropy Sorting (FFAVES). Use FFAVES to amplify the signal of groups of co-regulating genes in an unsupervised, multivariate manner. By amplifying the signal of genes with correlated expression, while filtering out genes that are randomly expressed, we can identify a subset of genes more predictive of different cell types. The output of FFAVES can then be used in our second algorithm, entropy sort feature weighting (ESFW), to create a ranked list of genes that are most likely to pertain to distinct sub-populations of cells in an scRNA-seq dataset.
homepage: https://github.com/aradley/FFAVES
version toolchain 2022.11.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FFC/","title":"FFC","text":"The FEniCS Form Compiler (FFC) is a compiler for finite element variational forms.
homepage: https://bitbucket.org/fenics-project/ffc
version versionsuffix toolchain 2018.1.0 -Python-3.6.4 foss/2018a 2019.1.0.post0 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FFLAS-FFPACK/","title":"FFLAS-FFPACK","text":"Finite Field Linear Algebra Subroutines / Package
homepage: https://linbox-team.github.io/fflas-ffpack/
version toolchain 2.2.0 foss/2016a 2.5.0 gfbf/2022a 2.5.0 gfbf/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FFTW.MPI/","title":"FFTW.MPI","text":"FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
homepage: https://www.fftw.org
version toolchain 3.3.10 gmpich/2024.06 3.3.10 gompi/2022.05 3.3.10 gompi/2022.10 3.3.10 gompi/2022a 3.3.10 gompi/2022b 3.3.10 gompi/2023.09 3.3.10 gompi/2023a 3.3.10 gompi/2023b 3.3.10 gompi/2024.05 3.3.10 gompi/2024a 3.3.10 nvompi/2022.07 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FFTW/","title":"FFTW","text":"FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
homepage: http://www.fftw.org
version versionsuffix toolchain 2.1.5 intel/2016b 2.1.5 intel/2017a 2.1.5 intel/2018b 3.3.10 GCC/11.3.0 3.3.10 GCC/12.2.0 3.3.10 GCC/12.3.0 3.3.10 GCC/13.2.0 3.3.10 GCC/13.3.0 3.3.10 NVHPC/22.7-CUDA-11.7.0 3.3.10 gompi/2021b 3.3.10 iimpi/2021b 3.3.10 iimpi/2022a 3.3.10 iimpi/2022b 3.3.4 gmpich/2016a 3.3.4 gmvapich2/1.7.20 3.3.4 gmvapich2/2016a 3.3.4 gompi/2016.04 3.3.4 gompi/2016.06 3.3.4 gompi/2016.07 3.3.4 gompi/2016a 3.3.4 gompi/2016b 3.3.4 intel/2016a 3.3.4 intel/2016b 3.3.5 gompi/2016.07 3.3.5 gompi/2016.09 3.3.5 gompi/2016b 3.3.5 intel/2016b 3.3.6 gimpi/2017b 3.3.6 gimpic/2017b 3.3.6 gompi/2017a 3.3.6 gompi/2017b 3.3.6 gompic/2017b 3.3.6 intel/2016b 3.3.6 intel/2017a 3.3.6 intel/2017b 3.3.6 intelcuda/2017b 3.3.7 -serial GCC/6.4.0-2.28 3.3.7 gimkl/2017a 3.3.7 gimpi/2018a 3.3.7 gmpich/2017.08 3.3.7 gompi/2018a 3.3.7 gompic/2018a 3.3.7 intel/2017b 3.3.7 intel/2018.00 3.3.7 intel/2018.01 3.3.7 intel/2018a 3.3.7 iomkl/2018a 3.3.8 -serial GCC/9.3.0 3.3.8 gompi/2018.08 3.3.8 gompi/2018b 3.3.8 gompi/2019a 3.3.8 gompi/2019b 3.3.8 -amd gompi/2020a 3.3.8 gompi/2020a 3.3.8 gompi/2020b 3.3.8 gompic/2018b 3.3.8 gompic/2019a 3.3.8 gompic/2019b 3.3.8 gompic/2020a 3.3.8 gompic/2020b 3.3.8 iimpi/2020b 3.3.8 intel/2018b 3.3.8 intel/2019a 3.3.8 intel/2019b 3.3.8 intel/2020a 3.3.8 intel/2020b 3.3.8 iomkl/2018b 3.3.8 iomkl/2020b 3.3.8 iompi/2020b 3.3.9 gompi/2021a 3.3.9 intel/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FFmpeg/","title":"FFmpeg","text":"A complete, cross-platform solution to record, convert and stream audio and video.
homepage: https://www.ffmpeg.org/
version toolchain 0.10.16 gimkl/2.11.5 0.10.16 intel/2016a 2.8.6 intel/2016a 2.8.7 foss/2016a 2.8.7 intel/2016a 3.0.2 foss/2016a 3.0.2 intel/2016a 3.1.3 foss/2016b 3.1.3 intel/2016b 3.2.4 gimkl/2017a 3.3.1 foss/2016b 3.3.4 intel/2017a 3.4 GCCcore/6.4.0 3.4.1 foss/2017b 3.4.1 intel/2017b 3.4.2 foss/2018a 3.4.2 intel/2018a 3.4.5 foss/2018b 4.0 foss/2018a 4.0 intel/2018a 4.0.1 intel/2018a 4.1 foss/2018b 4.1 fosscuda/2018b 4.1 intel/2018b 4.1.3 GCCcore/8.2.0 4.2.1 GCCcore/8.3.0 4.2.2 GCCcore/9.3.0 4.3.1 GCCcore/10.2.0 4.3.2 GCCcore/10.3.0 4.3.2 GCCcore/11.2.0 4.4.2 GCCcore/11.3.0 5.0.1 GCCcore/11.3.0 5.1.2 GCCcore/12.2.0 6.0 GCCcore/12.3.0 6.0 GCCcore/13.2.0 7.0.2 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FGSL/","title":"FGSL","text":"FGSL: A Fortran interface to the GNU Scientific Library
homepage: https://www.lrz.de/services/software/mathematik/gsl/fortran/
version toolchain 1.1.0 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FHI-aims/","title":"FHI-aims","text":"FHI-aims is an efficient, accurate all-electron, full-potential electronic structure code package for computational molecular and materials science (non-periodic and periodic systems). The code supports DFT (semilocal and hybrid) and many-body perturbation theory. FHI-aims is particularly efficient for molecular systems and nanostructures, while maintaining high numerical accuracy for all production tasks. Production calculations handle up to several thousand atoms and can efficiently use (ten) thousands of cores.
homepage: https://aimsclub.fhi-berlin.mpg.de/
version toolchain 200112_2 intel/2019b 221103 intel/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FIAT/","title":"FIAT","text":"The FInite element Automatic Tabulator FIAT supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.
homepage: https://bitbucket.org/fenics-project/fiat
version versionsuffix toolchain 1.6.0 -Python-2.7.11 foss/2016a 1.6.0 -Python-2.7.11 intel/2016a 2018.1.0 -Python-3.6.4 foss/2018a 2019.1.0 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FIGARO/","title":"FIGARO","text":"FIGARO: An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters.
homepage: https://github.com/Zymo-Research/figaro
version toolchain 1.1.2 intel/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FIRESTARTER/","title":"FIRESTARTER","text":"FIRESTARTER: A Processor Stress Test Utility. FIRESTARTER maximizes the energy consumption of 64-Bit x86 processors by generating heavy load on the execution units as well as transferring data between the cores and multiple levels of the memory hierarchy.
homepage: https://github.com/tud-zih-energy/FIRESTARTER/
version toolchain 2.0 gcccuda/2020a 2.0 gcccuda/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FIX/","title":"FIX","text":"FIX attempts to auto-classify ICA components into \"good\" vs \"bad\" components, so that the bad components can be removed from the 4D FMRI data.
homepage: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX
version versionsuffix toolchain 1.06.12 -Octave-Python-3.7.2 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FIt-SNE/","title":"FIt-SNE","text":"t-distributed stochastic neighbor embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we implement a heatmap-style visualization for scRNA-seq based on one-dimensional t-SNE for simultaneously visualizing the expression patterns of thousands of genes.
homepage: https://github.com/KlugerLab/FIt-SNE
version toolchain 1.1.0 gompi/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FLAC/","title":"FLAC","text":"FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality.
homepage: https://xiph.org/flac/
version toolchain 1.3.3 GCCcore/10.2.0 1.3.3 GCCcore/10.3.0 1.3.3 GCCcore/11.2.0 1.3.4 GCCcore/11.3.0 1.4.2 GCCcore/12.2.0 1.4.2 GCCcore/12.3.0 1.4.3 GCCcore/13.2.0 1.4.3 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FLAIR/","title":"FLAIR","text":"FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.
homepage: https://github.com/BrooksLabUCSC/flair
version versionsuffix toolchain 1.5 -Python-3.7.4 foss/2019b 1.5.1-20200630 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FLANN/","title":"FLANN","text":"FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces.
homepage: https://github.com/mariusmuja/flann/
version versionsuffix toolchain 1.8.4 -Python-3.8.2 foss/2020a 1.8.4 -Python-2.7.11 intel/2016a 1.8.4 -Python-2.7.14 intel/2017b 1.9.1 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FLASH/","title":"FLASH","text":"FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.
homepage: https://ccb.jhu.edu/software/FLASH/
version toolchain 1.2.11 GCC/8.3.0 1.2.11 foss/2016a 1.2.11 foss/2018a 1.2.11 foss/2018b 2.2.00 GCC/11.2.0 2.2.00 GCCcore/12.2.0 2.2.00 foss/2018b 2.2.00 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FLEUR/","title":"FLEUR","text":"FLEUR is a feature-full, freely available FLAPW (full potential linearized augmented planewave) code, based on density-functional theory.
homepage: http://www.flapw.de/
version toolchain 0.26e intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FLINT/","title":"FLINT","text":"FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested.
homepage: http://www.flintlib.org
version toolchain 2.5.2 GCC/7.3.0-2.30 2.5.2 GCC/8.2.0-2.31.1 2.5.2 GCC/8.3.0 2.5.2 iccifort/2018.3.222-GCC-7.3.0-2.30 2.7.1 GCC/10.3.0 2.8.4 foss/2021b 2.9.0 gfbf/2022a 2.9.0 gfbf/2022b 3.1.1 gfbf/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FLTK/","title":"FLTK","text":"FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.
homepage: http://www.fltk.org
version toolchain 1.3.3 foss/2016a 1.3.3 foss/2016b 1.3.3 intel/2016a 1.3.3 intel/2016b 1.3.4 foss/2017b 1.3.4 foss/2018a 1.3.4 foss/2018b 1.3.4 fosscuda/2017b 1.3.4 fosscuda/2018a 1.3.4 fosscuda/2018b 1.3.4 intel/2017a 1.3.4 intel/2017b 1.3.4 intel/2018a 1.3.4 intel/2018b 1.3.4 intelcuda/2017b 1.3.5 GCC/8.2.0-2.31.1 1.3.5 GCC/8.3.0 1.3.5 GCCcore/10.2.0 1.3.5 GCCcore/9.3.0 1.3.6 GCCcore/10.3.0 1.3.7 GCCcore/11.2.0 1.3.8 GCCcore/11.3.0 1.3.8 GCCcore/12.2.0 1.3.8 GCCcore/12.3.0 1.3.9 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FLUENT/","title":"FLUENT","text":"ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.
homepage: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent
version toolchain 14.5 system 15.0.7 system 16.0 system 17.1 system 18.0 system 18.1 system 18.2 system 2019R3 system 2021R1 system 2021R2 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FMILibrary/","title":"FMILibrary","text":"FMI library is intended as a foundation for applications interfacing FMUs (Functional Mockup Units) that follow FMI Standard. This version of the library supports FMI 1.0 and FMI2.0. See http://www.fmi-standard.org/
homepage: https://jmodelica.org/
version toolchain 2.0.3 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FMM3D/","title":"FMM3D","text":"Flatiron Institute Fast Multipole Libraries: a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a multi-core shared-memory machine.
homepage: https://fmm3d.readthedocs.io
version toolchain 1.0.4 foss/2023a 20211018 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FMPy/","title":"FMPy","text":"FMPy is a free Python library to simulate Functional Mock-up Units (FMUs).
homepage: https://github.com/CATIA-Systems/FMPy
version toolchain 0.3.2 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FMRIprep/","title":"FMRIprep","text":"FMRIprep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.
homepage: https://fmriprep.readthedocs.io
version versionsuffix toolchain 1.1.8 -Python-3.6.6 foss/2018b 1.4.1 -Python-3.6.6 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FMS/","title":"FMS","text":"The Flexible Modeling System (FMS) is a software framework for supporting the efficient development, construction, execution, and scientific interpretation of atmospheric, oceanic, and climate system models.
homepage: https://github.com/NOAA-GFDL/FMS
version toolchain 2022.02 gompi/2022a 2022.02 iimpi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FORD/","title":"FORD","text":"FORD is an automatic documentation generator for modern Fortran programs
homepage: https://github.com/Fortran-FOSS-Programmers/ford/wiki
version toolchain 6.1.1 GCCcore/10.2.0 6.1.15 GCCcore/11.3.0 6.1.6 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FOX-Toolkit/","title":"FOX-Toolkit","text":"FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively. It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulation. FOX also implements icons, images, and user-convenience features such as status line help, and tooltips.
homepage: https://www.fox-toolkit.org/
version toolchain 1.6.57 GCCcore/11.2.0 1.6.57 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FPM/","title":"FPM","text":"Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease and sanity.
homepage: https://github.com/jordansissel/fpm
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","boost":0.5},{"location":"version-specific/supported-software/f/FRANz/","title":"FRANz","text":"A fast and flexible parentage inference program for natural populations.
homepage: https://www.bioinf.uni-leipzig.de/Software/FRANz
version toolchain 2.0.0 foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FRUIT/","title":"FRUIT","text":"FORTRAN Unit Test Framework (FRUIT)
homepage: https://fortranxunit.sourceforge.io
version versionsuffix toolchain 3.4.3 -Ruby-2.5.1 foss/2018a 3.4.3 -Ruby-2.5.1 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FRUIT_processor/","title":"FRUIT_processor","text":"FORTRAN Unit Test Framework (FRUIT)
homepage: https://fortranxunit.sourceforge.io
version versionsuffix toolchain 3.4.3 -Ruby-2.5.1 foss/2018a 3.4.3 -Ruby-2.5.1 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FSL/","title":"FSL","text":"FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
homepage: http://www.fmrib.ox.ac.uk/fsl/
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","boost":0.5},{"location":"version-specific/supported-software/f/FSLeyes/","title":"FSLeyes","text":"FSLeyes is the FSL image viewer.
homepage: https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes
version versionsuffix toolchain 0.15.0 -Python-2.7.13 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FSON/","title":"FSON","text":"Fortran 95 JSON Parser
homepage: https://github.com/josephalevin/fson
version toolchain 1.0.5 GCC/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FTGL/","title":"FTGL","text":"FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications.
homepage: http://ftgl.sourceforge.net/docs/html/
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","boost":0.5},{"location":"version-specific/supported-software/f/FUNWAVE-TVD/","title":"FUNWAVE-TVD","text":"FUNWAVE\u2013TVD is the TVD version of the fully nonlinear Boussinesq wave model (FUNWAVE) initially developed by Kirby et al.
homepage: https://fengyanshi.github.io
version versionsuffix toolchain 3.1-20170525 -no-storm intel/2017a 3.1-20170525 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FUSE/","title":"FUSE","text":"The reference implementation of the Linux FUSE (Filesystem in Userspace) interface
homepage: https://github.com/libfuse/libfuse
version toolchain 3.14.1 GCCcore/11.3.0 3.14.1 GCCcore/12.2.0 3.16.2 GCCcore/12.3.0 3.2.6 intel/2018a 3.4.1 foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FabIO/","title":"FabIO","text":"FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers (as a python dictionary) and datasets (as a numpy ndarray of integers or floats).
homepage: http://www.silx.org
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","boost":0.5},{"location":"version-specific/supported-software/f/Faber/","title":"Faber","text":"Faber started as a clone of Boost.Build, to experiment with a new Python frontend. Meanwhile it has evolved into a new build system, which retains most of the features found in Boost.Build, but with (hopefully !) much simplified logic, in addition of course to using Python as scripting language, rather than Jam. The original bjam engine is still in use as scheduler, though at this point that is mostly an implementation detail.
homepage: https://stefanseefeld.github.io/faber
version toolchain 0.3 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/Faiss/","title":"Faiss","text":"Faiss is a library for efficient similarity search and clustering of dense vectors. It contains algorithms that search in sets of vectors of any size, up to ones that possibly do not fit in RAM. It also contains supporting code for evaluation and parameter tuning. Faiss is written in C++ with complete wrappers for Python/numpy. Some of the most useful algorithms are implemented on the GPU. It is developed primarily at Meta's Fundamental AI Research group.
homepage: https://github.com/facebookresearch/faiss
version versionsuffix toolchain 1.7.4 -CUDA-12.1.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FastANI/","title":"FastANI","text":"FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.
homepage: http://www.iodbc.org/
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","boost":0.5},{"location":"version-specific/supported-software/f/FastFold/","title":"FastFold","text":"Optimizing Protein Structure Prediction Model Training and Inference on GPU Clusters
homepage: https://github.com/hpcaitech/FastFold
version versionsuffix toolchain 20220729 -CUDA-11.3.1 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FastME/","title":"FastME","text":"FastME: a comprehensive, accurate and fast distance-based phylogeny inference program.
homepage: http://www.atgc-montpellier.fr/fastme/
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","boost":0.5},{"location":"version-specific/supported-software/f/FastQC/","title":"FastQC","text":"FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.
homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
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","boost":0.5},{"location":"version-specific/supported-software/f/FastQTL/","title":"FastQTL","text":"FastQTL is a QTL mapper
homepage: http://fastqtl.sourceforge.net/
version toolchain 2.184 GCC/11.2.0 2.184 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FastQ_Screen/","title":"FastQ_Screen","text":"FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
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","boost":0.5},{"location":"version-specific/supported-software/f/FastRFS/","title":"FastRFS","text":"Fast Robinson Foulds Supertrees
homepage: https://github.com/pranjalv123/FastRFS
version toolchain 1.0-20190613 gompi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FastTree/","title":"FastTree","text":"FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.
homepage: http://www.microbesonline.org/fasttree/
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","boost":0.5},{"location":"version-specific/supported-software/f/FastViromeExplorer/","title":"FastViromeExplorer","text":"Identify the viruses/phages and their abundance in the viral metagenomics data.
homepage: https://code.vt.edu/saima5/FastViromeExplorer
version toolchain 20180422 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FastaIndex/","title":"FastaIndex","text":"FastA index (.fai) handler compatible with samtools faidx
homepage: https://github.com/lpryszcz/FastaIndex
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","boost":0.5},{"location":"version-specific/supported-software/f/Fastaq/","title":"Fastaq","text":"Python3 scripts to manipulate FASTA and FASTQ files.
homepage: https://github.com/sanger-pathogens/Fastaq
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","boost":0.5},{"location":"version-specific/supported-software/f/Ferret/","title":"Ferret","text":"Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets.
homepage: http://ferret.pmel.noaa.gov/
version toolchain 7.3 intel/2017b 7.5.0 foss/2019b 7.6.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FigureGen/","title":"FigureGen","text":"FigureGen is a Fortran program that creates images for ADCIRC files. It reads mesh files (fort.14, etc.), nodal attributes files (fort.13, etc.) and output files (fort.63, fort.64, maxele.63, etc.). It plots contours, contour lines, and vectors. Using FigureGen, you can go directly from the ADCIRC input and output files to a presentation-quality figure, for one or multiple time snaps.
homepage: https://ccht.ccee.ncsu.edu/category/software/figuregen/
version toolchain 51-20190516 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/Fiji/","title":"Fiji","text":"Fiji is an image processing package\u2014a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. This release is based on ImageJ-2.1.0 and Fiji-2.1.1
homepage: https://fiji.sc
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","boost":0.5},{"location":"version-specific/supported-software/f/Filtlong/","title":"Filtlong","text":"Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter
homepage: https://github.com/rrwick/Filtlong
version toolchain 0.2.0 GCC/10.2.0 0.2.0 foss/2016b 0.2.1 GCC/10.3.0 0.2.1 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/Fiona/","title":"Fiona","text":"Fiona is designed to be simple and dependable. It focuses on reading and writing data in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS packages such as pyproj, Rtree, and Shapely.
homepage: https://github.com/Toblerity/Fiona
version versionsuffix toolchain 1.8.13 -Python-3.7.4 foss/2019b 1.8.13 -Python-3.7.4 fosscuda/2019b 1.8.13 -Python-3.7.4 intel/2019b 1.8.13.post1 -Python-3.7.2 foss/2019a 1.8.16 -Python-3.8.2 foss/2020a 1.8.20 foss/2020b 1.8.20 foss/2021a 1.8.20 intel/2020b 1.8.21 foss/2021b 1.8.21 foss/2022a 1.9.2 foss/2022b 1.9.5 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FireWorks/","title":"FireWorks","text":"FireWorks helps run calculation workflows, with a centralized workflow server controlling many worker nodes.
homepage: https://pypi.python.org/pypi/FireWorks
version versionsuffix toolchain 1.4.2 -Python-2.7.13 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/Firefox/","title":"Firefox","text":"Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the Mozilla code base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks.
homepage: https://www.mozilla.org/en-US/firefox/new/
version toolchain 44.0.2 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/Flask/","title":"Flask","text":"\" Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications.
homepage: https://www.palletsprojects.com/p/flask/
version versionsuffix toolchain 1.0.2 -Python-3.6.6 foss/2018b 1.1.2 GCCcore/10.2.0 1.1.2 -Python-3.7.4 GCCcore/8.3.0 1.1.2 -Python-3.8.2 GCCcore/9.3.0 1.1.4 GCCcore/10.3.0 2.0.2 GCCcore/11.2.0 2.2.2 GCCcore/11.3.0 2.2.3 GCCcore/12.2.0 2.3.3 GCCcore/12.3.0 3.0.0 GCCcore/13.2.0 3.0.3 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/Flax/","title":"Flax","text":"Flax is a high-performance neural network library and ecosystem for JAX that is designed for flexibility: Try new forms of training by forking an example and by modifying the training loop, not by adding features to a framework.
homepage: https://flax.readthedocs.io
version versionsuffix toolchain 0.8.4 -CUDA-12.1.1 gfbf/2023a 0.8.4 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/Flexbar/","title":"Flexbar","text":"The program Flexbar preprocesses high-throughput sequencing data efficiently
homepage: https://github.com/seqan/flexbar
version toolchain 3.5.0 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FlexiBLAS/","title":"FlexiBLAS","text":"FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.
homepage: https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release
version toolchain 3.0.4 GCC/10.3.0 3.0.4 GCC/11.2.0 3.1.3 GCC/11.2.0 3.2.0 GCC/11.3.0 3.2.0 NVHPC/22.7-CUDA-11.7.0 3.2.1 GCC/12.2.0 3.3.1 GCC/12.3.0 3.3.1 GCC/13.2.0 3.4.4 GCC/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FlexiDot/","title":"FlexiDot","text":"Highly customizable, ambiguity-aware dotplots for visual sequence analyses
homepage: https://github.com/molbio-dresden/flexidot
version versionsuffix toolchain 1.06 -Python-2.7.15 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/Flink/","title":"Flink","text":"Apache Flink is a framework and distributed processing engine for stateful computations over unbounded and bounded data streams. Flink has been designed to run in all common cluster environments, perform computations at in-memory speed and at any scale.
homepage: https://flink.apache.org/
version versionsuffix toolchain 1.11.2 -bin-scala_2.11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/Flye/","title":"Flye","text":"Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.
homepage: https://github.com/fenderglass/Flye
version versionsuffix toolchain 2.4 -Python-2.7.15 intel/2018b 2.6 -Python-3.7.2 foss/2019a 2.6 -Python-3.7.4 intel/2019b 2.8.1 -Python-3.8.2 intel/2020a 2.8.2 -Python-3.8.2 foss/2020a 2.8.3 GCC/10.2.0 2.8.3 iccifort/2020.4.304 2.9 GCC/10.3.0 2.9 intel-compilers/2021.2.0 2.9.1 GCC/11.2.0 2.9.2 GCC/11.3.0 2.9.3 GCC/10.3.0 2.9.3 GCC/12.3.0 2.9.4 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FoBiS/","title":"FoBiS","text":"A Fortran Building System for automatic building modern Fortran projects
homepage: https://github.com/szaghi/FoBiS
version toolchain 3.0.5 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FoX/","title":"FoX","text":"FoX is an XML library written in Fortran 95. It allows software developers to read, write and modify XML documents from Fortran applications without the complications of dealing with multi-language development.
homepage: http://homepages.see.leeds.ac.uk/~earawa/FoX/
version toolchain 4.1.2 GCC/11.2.0 4.1.2 GCC/9.3.0 4.1.2 intel/2017b 4.1.2 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FoldX/","title":"FoldX","text":"FoldX is used to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.
homepage: http://foldx.crg.es/
version toolchain 2.5.2 system 3.0-beta5.1 system 3.0-beta6.1 system 3.0-beta6 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FragGeneScan/","title":"FragGeneScan","text":"FragGeneScan is an application for finding (fragmented) genes in short reads.
homepage: https://omics.informatics.indiana.edu/FragGeneScan/
version toolchain 1.31 GCCcore/10.2.0 1.31 GCCcore/10.3.0 1.31 GCCcore/11.2.0 1.31 GCCcore/11.3.0 1.31 GCCcore/12.3.0 1.31 GCCcore/8.2.0 1.31 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FragPipe/","title":"FragPipe","text":"FragPipe is a Java Graphical User Interface (GUI) for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data.
homepage: https://fragpipe.nesvilab.org
version versionsuffix toolchain 20.0 -Java-11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FreeBarcodes/","title":"FreeBarcodes","text":"A package for the generation and decoding of FREE divergence error-correcting DNA barcodes
homepage: https://github.com/hawkjo/freebarcodes
version toolchain 3.0.a5 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FreeFEM/","title":"FreeFEM","text":"FreeFEM offers a fast interpolation algorithm and a language for the manipulation of data on multiple meshes.
homepage: https://freefem.org
version versionsuffix toolchain 4.5 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FreeFem%2B%2B/","title":"FreeFem++","text":"FreeFem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D.
homepage: http://www.freefem.org/
version versionsuffix toolchain 3.58 -downloaded-deps foss/2017b 3.60 -downloaded-deps intel/2018a 3.61-1 -downloaded-deps intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FreeImage/","title":"FreeImage","text":"FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to use, fast, multithreading safe.
homepage: http://freeimage.sourceforge.net
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","boost":0.5},{"location":"version-specific/supported-software/f/FreeSASA/","title":"FreeSASA","text":"FreeSASA is a command line tool, C-library and Python module for calculating solvent accessible surface areas (SASA).
homepage: https://freesasa.github.io
version toolchain 2.0.3 GCC/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FreeSurfer/","title":"FreeSurfer","text":"FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.
homepage: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki
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","boost":0.5},{"location":"version-specific/supported-software/f/FreeTDS/","title":"FreeTDS","text":"FreeTDS is a set of libraries for Unix and Linux that allows your programs to natively talk to Microsoft SQL Server and Sybase databases.
homepage: https://www.freetds.org/
version toolchain 1.3.3 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FreeXL/","title":"FreeXL","text":"FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.
homepage: https://www.gaia-gis.it/fossil/freexl/index
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","boost":0.5},{"location":"version-specific/supported-software/f/FriBidi/","title":"FriBidi","text":"FriBidi is a free implementation of the Unicode Bidirectional (BiDi) Algorithm. It also provides utility functions to aid in the development of interactive editors and widgets that implement BiDi functionality. The BiDi algorithm is a prerequisite for supporting right-to-left scripts such as Hebrew, Arabic, Syriac, and Thaana.
homepage: https://directory.fsf.org/wiki/Fribidi
version toolchain 1.0.1 foss/2018a 1.0.1 intel/2018a 1.0.10 GCCcore/10.2.0 1.0.10 GCCcore/10.3.0 1.0.10 GCCcore/11.2.0 1.0.12 GCCcore/11.3.0 1.0.12 GCCcore/12.2.0 1.0.12 GCCcore/12.3.0 1.0.13 GCCcore/13.2.0 1.0.15 GCCcore/13.3.0 1.0.2 GCCcore/6.4.0 1.0.5 GCCcore/7.3.0 1.0.5 GCCcore/8.2.0 1.0.5 GCCcore/8.3.0 1.0.9 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FuSeq/","title":"FuSeq","text":"FuSeq is a novel method to discover fusion genes from paired-end RNA sequencing data.
homepage: https://github.com/nghiavtr/FuSeq
version toolchain 1.1.2 gompi/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FunGAP/","title":"FunGAP","text":"Fungal Genome Annotation Pipeline using evidence-based gene model evaluation.
homepage: https://github.com/CompSynBioLab-KoreaUniv/FunGAP
version toolchain 1.1.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/FusionCatcher/","title":"FusionCatcher","text":"FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end or single-end reads from Illumina NGS platforms like Solexa/HiSeq/NextSeq/MiSeq/MiniSeq) from diseased samples.
homepage: https://github.com/ndaniel/fusioncatcher
version versionsuffix toolchain 1.20 -Python-2.7.16 foss/2019b 1.30 -Python-2.7.16 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/f90cache/","title":"f90cache","text":"f90cache is a compiler cache. It acts as a caching pre-processor to Fortran compilers, using the -E compiler switch and a hash to detect when a compilation can be satisfied from cache. This often results in a great speedup in common compilations.
homepage: http://people.irisa.fr/Edouard.Canot/f90cache/
version toolchain 0.96 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/f90nml/","title":"f90nml","text":"A Python module and command line tool for parsing Fortran namelist files
homepage: https://github.com/marshallward/f90nml
version toolchain 1.4.4 GCCcore/12.2.0 1.4.4 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/f90wrap/","title":"f90wrap","text":"f90wrap is a tool to automatically generate Python extension modules which interface to Fortran code that makes use of derived types. It builds on the capabilities of the popular f2py utility by generating a simpler Fortran 90 interface to the original Fortran code which is then suitable for wrapping with f2py, together with a higher-level Pythonic wrapper that makes the existance of an additional layer transparent to the final user.
homepage: https://github.com/jameskermode/f90wrap
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","boost":0.5},{"location":"version-specific/supported-software/f/faceswap/","title":"faceswap","text":"Faceswap is a tool that utilizes deep learning to recognize and swap faces in pictures and videos.
homepage: https://github.com/deepfakes/faceswap
version versionsuffix toolchain 20180212 -Python-3.6.3 foss/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fast5/","title":"fast5","text":"A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.
homepage: http://simpsonlab.github.io/2017/02/27/packing_fast5/
version toolchain 0.6.5 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fastPHASE/","title":"fastPHASE","text":"fastPHASE: software for haplotype reconstruction, and estimating missing genotypes from population data Documentation: http://scheet.org/code/fastphase_doc_1.4.pdf
homepage: http://stephenslab.uchicago.edu/software.html#fastphase
version toolchain 1.4.8 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fastStructure/","title":"fastStructure","text":"fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.
homepage: http://rajanil.github.io/fastStructure/
version versionsuffix toolchain 1.0 -Python-2.7.11 foss/2016a 1.0 -Python-2.7.12 foss/2016b 1.0 -Python-2.7.13 foss/2017a 1.0 -Python-2.7.15 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fasta-reader/","title":"fasta-reader","text":"FASTA file reader
homepage: https://github.com/EBI-Metagenomics/fasta-reader-py
version toolchain 3.0.2 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fastahack/","title":"fastahack","text":"Utilities for indexing and sequence extraction from FASTA files.
homepage: https://github.com/ekg/fastahack
version toolchain 1.0.0 GCCcore/10.2.0 1.0.0 GCCcore/10.3.0 1.0.0 GCCcore/11.2.0 1.0.0 GCCcore/11.3.0 1.0.0 GCCcore/12.2.0 1.0.0 GCCcore/12.3.0 1.0.0 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fastai/","title":"fastai","text":"The fastai deep learning library.
homepage: https://www.fast.ai/
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","boost":0.5},{"location":"version-specific/supported-software/f/fastfilters/","title":"fastfilters","text":"Fast gaussian and derivative convolutional filters.
homepage: https://github.com/ilastik/fastfilters/
version toolchain 0.3 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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","boost":0.5},{"location":"version-specific/supported-software/f/fmt/","title":"fmt","text":"fmt (formerly cppformat) is an open-source formatting library.
homepage: http://fmtlib.net/
version toolchain 10.0.0 GCCcore/12.3.0 10.1.0 GCCcore/12.3.0 10.2.0 GCCcore/13.2.0 10.2.1 GCCcore/13.2.0 3.0.1 foss/2016b 3.0.1 intel/2016b 3.0.2 GCCcore/6.4.0 3.0.2 intel/2017a 5.3.0 GCCcore/7.3.0 5.3.0 GCCcore/8.2.0 6.2.1 GCCcore/9.3.0 7.0.3 GCCcore/9.3.0 7.1.1 GCCcore/11.2.0 8.1.1 GCCcore/11.2.0 9.1.0 GCCcore/11.3.0 9.1.0 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fontconfig/","title":"fontconfig","text":"Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
homepage: http://www.freedesktop.org/software/fontconfig
version versionsuffix toolchain 2.11.94 foss/2016a 2.11.94 intel/2016a 2.11.95 foss/2016a 2.11.95 intel/2016a 2.12.1 GCCcore/5.4.0 2.12.1 -libpng-1.6.29 GCCcore/6.3.0 2.12.1 GCCcore/6.3.0 2.12.1 foss/2016b 2.12.1 gimkl/2017a 2.12.1 intel/2016b 2.12.4 GCCcore/6.4.0 2.12.6 GCCcore/6.4.0 2.13.0 GCCcore/6.4.0 2.13.0 GCCcore/7.3.0 2.13.1 GCCcore/8.2.0 2.13.1 GCCcore/8.3.0 2.13.92 GCCcore/10.2.0 2.13.92 GCCcore/9.3.0 2.13.93 GCCcore/10.3.0 2.13.94 GCCcore/11.2.0 2.14.0 GCCcore/11.3.0 2.14.1 GCCcore/12.2.0 2.14.2 GCCcore/12.3.0 2.14.2 GCCcore/13.2.0 2.15.0 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fontsproto/","title":"fontsproto","text":"X11 font extension wire protocol
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 2.1.3 foss/2016a 2.1.3 gimkl/2.11.5 2.1.3 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fonttools/","title":"fonttools","text":"fontTools is a library for manipulating fonts, written in Python. The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX. It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.
homepage: https://python-markdown.github.io/
version toolchain 4.53.1 GCCcore/11.3.0 4.53.1 GCCcore/12.2.0 4.53.1 GCCcore/12.3.0 4.53.1 GCCcore/13.2.0 4.53.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/forbear/","title":"forbear","text":"A Fortran Library for building and running fancy progress bar
homepage: https://github.com/szaghi/forbear
version toolchain 1.2.0 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/foss/","title":"foss","text":"GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
homepage: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain
version toolchain 2016.04 system 2016.06 system 2016.07 system 2016.09 system 2016a system 2016b system 2017a system 2017b system 2018.08 system 2018a system 2018b system 2019a system 2019b system 2020a system 2020b system 2021a system 2021b system 2022.05 system 2022.10 system 2022a system 2022b system 2023.09 system 2023a system 2023b system 2024.05 system 2024a system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fosscuda/","title":"fosscuda","text":"GCC based compiler toolchain with CUDA support, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
homepage: <(none)>
version toolchain 2017b system 2018a system 2018b system 2019a system 2019b system 2020a system 2020b system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fplll/","title":"fplll","text":"fplll contains implementations of several lattice algorithms. The implementation relies on floating-point orthogonalization, and the 1982 paper from Lenstra, Lenstra Jr. and Lovasz (LLL) is central to the code, hence the name.
homepage: https://github.com/fplll/fplll
version toolchain 5.4.5 GCCcore/11.3.0 5.4.5 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fpocket/","title":"fpocket","text":"The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.
homepage: https://github.com/Discngine/fpocket
version toolchain 3.1.4.2 gompi/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fpylll/","title":"fpylll","text":"A Python wrapper for fplll.
homepage: https://pypi.org/project/fpylll
version toolchain 0.5.9 foss/2022a 0.6.1 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fqtrim/","title":"fqtrim","text":"fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, terminal unknown bases (Ns) and low quality 3' regions in reads from high-throughput next-generation sequencing machines.
homepage: http://ccb.jhu.edu/software/fqtrim/
version toolchain 0.9.4 intel/2016b 0.9.5 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fqzcomp/","title":"fqzcomp","text":"Fqzcomp is a basic fastq compressor, designed primarily for high performance. Despite that it is comparable to bzip2 for compression levels.
homepage: http://sourceforge.net/projects/fqzcomp/
version toolchain 4.6 GCC/4.8.2 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/freebayes/","title":"freebayes","text":"Bayesian haplotype-based genetic polymorphism discovery and genotyping.
homepage: https://github.com/freebayes/freebayes
version versionsuffix toolchain 1.3.5 GCC/10.2.0 1.3.5 -Python-3.8.2 GCC/9.3.0 1.3.6 -R-4.1.0 foss/2021a 1.3.6 -R-4.1.2 foss/2021b 1.3.7 -R-4.3.2 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/freeglut/","title":"freeglut","text":"freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.
homepage: http://freeglut.sourceforge.net/
version versionsuffix toolchain 3.0.0 GCCcore/8.2.0 3.0.0 -Mesa-11.2.1 foss/2016a 3.0.0 foss/2016a 3.0.0 foss/2016b 3.0.0 foss/2017b 3.0.0 foss/2018a 3.0.0 foss/2018b 3.0.0 -Mesa-11.2.1 intel/2016a 3.0.0 intel/2016a 3.0.0 intel/2016b 3.0.0 intel/2017a 3.0.0 intel/2017b 3.0.0 intel/2018a 3.2.1 GCCcore/10.2.0 3.2.1 GCCcore/10.3.0 3.2.1 GCCcore/11.2.0 3.2.1 GCCcore/8.3.0 3.2.1 GCCcore/9.3.0 3.2.2 GCCcore/11.3.0 3.4.0 GCCcore/12.2.0 3.4.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/freetype-py/","title":"freetype-py","text":"Python binding for the freetype library
homepage: https://github.com/rougier/freetype-py
version versionsuffix toolchain 2.2.0 -Python-3.7.4 GCCcore/8.3.0 2.4.0 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/freetype/","title":"freetype","text":"FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.
homepage: https://www.freetype.org
version versionsuffix toolchain 2.10.1 GCCcore/8.3.0 2.10.1 GCCcore/9.3.0 2.10.3 GCCcore/10.2.0 2.10.4 GCCcore/10.3.0 2.11.0 GCCcore/11.2.0 2.12.1 GCCcore/11.3.0 2.12.1 GCCcore/12.2.0 2.13.0 GCCcore/12.3.0 2.13.2 GCCcore/13.2.0 2.13.2 GCCcore/13.3.0 2.6.2 foss/2016a 2.6.2 gimkl/2.11.5 2.6.2 intel/2016a 2.6.3 foss/2016a 2.6.3 intel/2016a 2.6.5 GCCcore/4.9.3 2.6.5 GCCcore/5.4.0 2.6.5 foss/2016b 2.6.5 intel/2016b 2.7 foss/2016b 2.7 intel/2016b 2.7.1 GCCcore/5.4.0 2.7.1 -libpng-1.6.29 GCCcore/6.3.0 2.7.1 GCCcore/6.3.0 2.7.1 gimkl/2017a 2.7.1 intel/2016b 2.8 GCCcore/6.4.0 2.8.1 GCCcore/6.4.0 2.9 GCCcore/6.4.0 2.9.1 GCCcore/7.3.0 2.9.1 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/freud-analysis/","title":"freud-analysis","text":"The freud Python library provides a simple, flexible, powerful set of tools for analyzing trajectories obtained from molecular dynamics or Monte Carlo simulations. High performance, parallelized C++ is used to compute standard tools such as radial distribution functions, correlation functions, order parameters, and clusters, as well as original analysis methods including potentials of mean force and torque (PMFTs) and local environment matching. The freud library supports many input formats and outputs NumPy arrays, enabling integration with the scientific Python ecosystem for many typical materials science workflows.
homepage: https://github.com/glotzerlab/freud
version toolchain 2.6.2 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fsm-lite/","title":"fsm-lite","text":"A singe-core implemetation of frequency-based substring mining.
homepage: https://github.com/nvalimak/fsm-lite
version toolchain 1.0 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fsom/","title":"fsom","text":"A tiny C library for managing SOM (Self-Organizing Maps) neural networks.
homepage: https://github.com/ekg/fsom
version toolchain 20141119 GCCcore/10.2.0 20141119 GCCcore/10.3.0 20141119 GCCcore/11.2.0 20141119 GCCcore/9.3.0 20151117 GCCcore/11.3.0 20151117 GCCcore/12.2.0 20151117 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/ftfy/","title":"ftfy","text":"ftfy (fixes text for you) fixes Unicode that\u2019s broken in various ways. The goal of ftfy is to take in bad Unicode and output good Unicode, for use in your Unicode-aware code. This is different from taking in non-Unicode and outputting Unicode, which is not a goal of ftfy. It also isn\u2019t designed to protect you from having to write Unicode-aware code. ftfy helps those who help themselves.
homepage: http://ftfy.readthedocs.org
version toolchain 6.1.1 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fugue/","title":"fugue","text":"Fugue is a unified interface for distributed computing that lets users execute Python, Pandas, and SQL code on Spark, Dask, and Ray with minimal rewrites. Fugue is most commonly used for: Parallelizing or scaling existing Python and Pandas code by bringing it to Spark, Dask, or Ray with minimal rewrites. Using FugueSQL to define end-to-end workflows on top of Pandas, Spark, and Dask DataFrames. FugueSQL is an enhanced SQL interface that can invoke Python code.
homepage: https://github.com/fugue-project/fugue
version toolchain 0.8.7 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fullrmc/","title":"fullrmc","text":"Reverse Monte Carlo (RMC) is probably best known for its applications in condensed matter physics and solid state chemistry. fullrmc which stands for FUndamental Library Language for Reverse Monte Carlo is different than traditional RMC but a stochastic modelling method to solve an inverse problem whereby an atomic/molecular model is adjusted until its atoms position havei the greatest consistency with a set of experimental data.
homepage: https://bachiraoun.github.io/fullrmc
version versionsuffix toolchain 3.2.0 -Python-2.7.14 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fumi_tools/","title":"fumi_tools","text":"This tool is intended to deduplicate UMIs from single-end and paired-end sequencing data. Reads are considered identical when their UMIs have the same sequence, they have the same length and map at the same position.
homepage: https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools
version versionsuffix toolchain 0.18.2 GCC/10.3.0 0.18.2 GCC/11.2.0 0.18.2 -Python-3.6.6 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/funannotate/","title":"funannotate","text":"funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes)
homepage: https://funannotate.readthedocs.io
version toolchain 1.8.13 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/futhark/","title":"futhark","text":"Futhark is a small programming language designed to be compiled to efficient parallel code. It is a statically typed, data-parallel, and purely functional array language in the ML family, and comes with a heavily optimising ahead-of-time compiler that presently generates GPU code via CUDA and OpenCL, although the language itself is hardware-agnostic and can also run on multicore CPUs
homepage: https://futhark-lang.org/
version toolchain 0.19.5 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/futile/","title":"futile","text":"The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules and wrapper that encapsulate the most common low-level operations of a Fortran code.
homepage: https://launchpad.net/futile
version toolchain 1.8.3 foss/2020b 1.8.3 foss/2021a 1.8.3 foss/2021b 1.8.3 foss/2022a 1.8.3 intel/2020b 1.8.3 intel/2021a 1.8.3 intel/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/future/","title":"future","text":"python-future is the missing compatibility layer between Python 2 and Python 3.
homepage: https://python-future.org/
version versionsuffix toolchain 0.16.0 -Python-2.7.14 foss/2018a 0.16.0 -Python-2.7.15 foss/2018b 0.16.0 -Python-3.6.6 foss/2018b 0.16.0 -Python-2.7.14 intel/2017b 0.16.0 -Python-3.6.3 intel/2017b 0.16.0 -Python-2.7.14 intel/2018a 0.16.0 -Python-2.7.15 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/f/fxtract/","title":"fxtract","text":"Extract sequences from a fastx (fasta or fastq) file given a subsequence.
homepage: https://github.com/ctSkennerton/fxtract
version toolchain 2.3 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/","title":"List of supported software (g)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- G-PhoCS
- g2clib
- g2lib
- g2log
- Gaia
- GAMESS-US
- gap
- GapCloser
- GapFiller
- gappa
- GAPPadder
- GARLI
- garnett
- GAT
- GATB-Core
- GATE
- GATK
- Gaussian
- gawk
- gbasis
- Gblocks
- GBprocesS
- gbs2ploidy
- gc
- GC3Pie
- GCC
- GCCcore
- gcccuda
- gcloud
- GConf
- gcsfs
- GCTA
- Gctf
- GD
- GDAL
- GDB
- gdbgui
- gdbm
- gdc-client
- GDCHART
- GDCM
- GDGraph
- gdist
- Gdk-Pixbuf
- GDMA
- GDRCopy
- Gdspy
- Geant4
- Geant4-data
- gearshifft
- GEGL
- GEM
- GEM-library
- gemelli
- GEMMA
- gemmi
- gencore_variant_detection
- GeneMark-ET
- GenerativeModels
- gengetopt
- GenMap
- Genome_Profiler
- GenomeComb
- GenomeMapper
- genomepy
- GenomeTester4
- GenomeThreader
- GenomeTools
- GenomeWorks
- GenotypeHarmonizer
- genozip
- gensim
- geocube
- GeoDict
- geopandas
- geopy
- georges
- GEOS
- geosphere
- Gerris
- GETORB
- GetOrganelle
- gettext
- gexiv2
- gfbf
- GFF3-toolkit
- GffCompare
- gffread
- gffutils
- gflags
- GFOLD
- gh
- GHC
- Ghostscript
- GI-DocGen
- giac
- Gibbs2
- giflib
- gifsicle
- GIMIC
- gimkl
- GimmeMotifs
- GIMP
- gimpi
- gimpic
- GIMPS
- giolf
- giolfc
- Giotto-Suite
- git
- git-annex
- git-extras
- git-lfs
- GitPython
- Givaro
- Giza
- GKeyll
- GKlib-METIS
- gkmSVM
- GL2PS
- Glade
- glew
- GLFW
- GLI
- GLib
- glib-networking
- glibc
- GLibmm
- GLIMMER
- GlimmerHMM
- GLIMPSE
- GLM
- GLM-AED
- GlobalArrays
- Globus-CLI
- GlobusConnectPersonal
- glog
- GLPK
- glproto
- Glucose
- GMAP-GSNAP
- GMP
- GMP-ECM
- gmpflf
- gmpich
- gmpolf
- gmpy2
- gmsh
- GMT
- gmvapich2
- gmvolf
- GNU
- gnupg-bundle
- gnuplot
- GnuTLS
- Go
- goalign
- GOATOOLS
- gobff
- GObject-Introspection
- goblf
- GOBNILP
- Godon
- gofasta
- golf
- GOMC
- gomkl
- gompi
- gompic
- google-java-format
- googletest
- gotree
- GP2C
- GPAW
- GPAW-setups
- gperf
- gperftools
- GPflow
- gpustat
- GPy
- GPyOpt
- GPyTorch
- Grace
- Gradle
- gradunwarp
- graph-tool
- GraphDB
- Graphene
- GraphicsMagick
- graphite2
- GraPhlAn
- GraphMap
- GraphMap2
- Graphviz
- graphviz-python
- GRASP
- GRASP-suite
- GRASS
- Greenlet
- Grep
- gretl
- grib_api
- grid
- GRIDSS
- GRIT
- GRNBoost
- groff
- GroIMP
- GROMACS
- GromacsWrapper
- Groovy
- gRPC
- grpcio
- GSD
- GSEA
- gsettings-desktop-schemas
- GSL
- gSOAP
- gspell
- gsport
- GST-plugins-bad
- GST-plugins-base
- GStreamer
- gsutil
- gsw
- GTDB-Tk
- GTK+
- gtk-doc
- GTK2
- GTK3
- GTK4
- GtkSourceView
- GTOOL
- GTS
- Gubbins
- guenomu
- GUIDANCE
- Guile
- GULP
- Gurobi
- GUSHR
- Gymnasium
- gzip
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/G-PhoCS/","title":"G-PhoCS","text":"G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences. G-PhoCS accepts as input a set of multiple sequence alignments from separate neutrally evolving loci along the genome. Parameter inference is done in a Bayesian manner, using a Markov Chain Monte Carlo (MCMC) to jointly sample model parameters and genealogies at the input loci.
homepage: http://compgen.cshl.edu/GPhoCS/
version toolchain 1.2.3 iccifort/2019.1.144-GCC-8.2.0-2.31.1 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GAMESS-US/","title":"GAMESS-US","text":"The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.
homepage: http://www.msg.chem.iastate.edu/gamess/index.html
version versionsuffix toolchain 20141205-R1 intel/2016a 20170420-R1 -sockets intel/2016b 20170420-R1 intel/2016b 20180214-R1 -sockets foss/2016b 20180214-R1 foss/2016b 20220930-R2 gompi/2022a 20230930-R2 gompi/2022a 20230930-R2 intel-compilers/2022.1.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GAPPadder/","title":"GAPPadder","text":"GAPPadder is tool for closing gaps on draft genomes with short sequencing data
homepage: https://github.com/simoncchu/GAPPadder
version versionsuffix toolchain 20170601 -Python-2.7.18 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GARLI/","title":"GARLI","text":"GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for inferring phylogenetic trees. Using an approach similar to a classical genetic algorithm, it rapidly searches the space of evolutionary trees and model parameters to find the solution maximizing the likelihood score. It implements nucleotide, amino acid and codon-based models of sequence evolution, and runs on all platforms.
homepage: https://code.google.com/archive/p/garli/
version toolchain 2.01 gompi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GAT/","title":"GAT","text":"The Genomic Association Tester (GAT) is a tool for computing the significance of overlap between multiple sets of genomic intervals. GAT estimates significance based on simulation.
homepage: https://gat.readthedocs.io/
version versionsuffix toolchain 1.2.2 -Python-2.7.11 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GATB-Core/","title":"GATB-Core","text":"GATB-Core is a high-performance and low memory footprint C++ library that provides a set of highly efficient algorithms to analyse NGS data sets
homepage: https://gatb.inria.fr/software/gatb-core
version toolchain 1.4.2 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GATE/","title":"GATE","text":"GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography
homepage: http://www.opengatecollaboration.org/
version versionsuffix toolchain 6.2 -Python-2.7.11 intel/2016a 7.1 -Python-2.7.11 intel/2016a 7.2 -Python-2.7.11 intel/2016a 8.0 -Python-2.7.14 foss/2017b 8.0 -Python-2.7.14-Geant4-10.04 intel/2017b 8.0 -Python-2.7.14 intel/2017b 8.1.p01 -Python-2.7.15 foss/2018b 8.2 -Python-2.7.14 foss/2017b 8.2 -Python-2.7.15 foss/2018b 8.2 -Python-2.7.14 intel/2017b 9.0 -Python-3.7.4 foss/2019b 9.1 foss/2021b 9.2 foss/2021b 9.2 foss/2022a 9.4 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GATK/","title":"GATK","text":"The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.
homepage: http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit
version versionsuffix toolchain 1.0.5083 system 2.5-2 -Java-1.7.0_10 system 2.6-5 -Java-1.7.0_10 system 2.7-4 -Java-1.7.0_10 system 2.7-4 system 2.8-1 -Java-1.7.0_10 system 3.0-0 -Java-1.7.0_10 system 3.3-0 -Java-1.7.0_21 system 3.3-0 -Java-1.7.0_80 system 3.3-0 -Java-1.8.0_66 system 3.5 -Java-1.8.0_66 system 3.5 -Java-1.8.0_74 system 3.6 -Java-1.8.0_92 system 3.7 -Java-1.8.0_112 system 3.8-0 -Java-1.8.0_144 system 4.0.1.2 -Java-1.8 system 4.0.10.0 -Python-3.6.6 foss/2018b 4.0.12.0 -Python-3.6.6 foss/2018b 4.0.4.0 -Python-2.7.14 intel/2018a 4.0.4.0 -Python-3.6.4 intel/2018a 4.0.5.1 -Python-3.6.4 foss/2018a 4.0.7.0 -Python-2.7.14 intel/2018a 4.0.7.0 -Python-3.6.4 intel/2018a 4.0.8.1 -Python-2.7.15 foss/2018b 4.0.8.1 -Python-3.6.6 foss/2018b 4.1.0.0 -Python-3.6.6 foss/2018b 4.1.2.0 -Java-1.8 GCCcore/8.2.0 4.1.3.0 -Java-1.8 GCCcore/8.3.0 4.1.4.1 -Java-1.8 GCCcore/8.3.0 4.1.4.1 -Java-11 GCCcore/8.3.0 4.1.5.0 -Java-1.8 GCCcore/9.3.0 4.1.5.0 -Java-11 GCCcore/9.3.0 4.1.8.1 -Java-1.8 GCCcore/9.3.0 4.2.0.0 -Java-1.8 GCCcore/10.2.0 4.2.0.0 -Java-11 GCCcore/10.2.0 4.2.3.0 -Java-11 GCCcore/11.2.0 4.2.5.0 -Java-11 GCCcore/11.2.0 4.2.6.1 -Java-11 GCCcore/10.3.0 4.2.6.1 -Java-11 GCCcore/11.2.0 4.3.0.0 -Java-11 GCCcore/11.3.0 4.4.0.0 -Java-17 GCCcore/12.2.0 4.4.0.0 -Java-17 GCCcore/12.3.0 4.5.0.0 -Java-17 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GBprocesS/","title":"GBprocesS","text":"GBprocesS allows for the extraction of genomic inserts from NGS data for GBS experiments. Preprocessing is performed in different stages that are part of a linear pipeline where the steps are performed in order. GBprocesS provides a flexible way to adjust the functionality to your needs, as the operations required and the execution order vary depending on the GBS protocol used.
homepage: https://gbprocess.readthedocs.io/
version versionsuffix toolchain 2.3 -Python-3.8.2 intel/2020a 4.0.0.post1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GC3Pie/","title":"GC3Pie","text":"GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments.
homepage: https://gc3pie.readthedocs.org
version toolchain 2.4.2 system 2.5.0 system 2.5.2 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GCC/","title":"GCC","text":"The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
homepage: https://gcc.gnu.org/
version versionsuffix toolchain 10.1.0 system 10.2.0 system 10.3.0 system 11.1.0 system 11.2.0 system 11.3.0 system 11.4.0 system 12.1.0 system 12.2.0 system 12.3.0 system 13.1.0 system 13.2.0 system 13.3.0 system 14.1.0 system 14.2.0 system 4.8.1 -CLooG system 4.8.1 system 4.8.2 -CLooG-multilib system 4.8.2 -CLooG system 4.8.2 -multilib system 4.8.2 system 4.8.3 -CLooG-multilib system 4.8.3 system 4.8.4 -CLooG-multilib system 4.8.4 -CLooG system 4.8.4 system 4.8.5 system 4.9.0 -CLooG-multilib system 4.9.0 -CLooG system 4.9.0 system 4.9.1 -CLooG-multilib system 4.9.1 -CLooG system 4.9.1 system 4.9.2 -CLooG-multilib system 4.9.2 -CLooG system 4.9.2 -binutils-2.25 system 4.9.2 system 4.9.3 -2.25 system 4.9.3 -binutils-2.25 system 4.9.3 system 4.9.4 -2.25 system 5.1.0 -binutils-2.25 system 5.1.0 system 5.2.0 system 5.3.0 -2.26 system 5.3.0 system 5.4.0 -2.26 system 5.5.0 -2.26 system 6.1.0 -2.27 system 6.2.0 -2.27 system 6.3.0 -2.27 system 6.3.0 -2.28 system 6.4.0 -2.28 system 7.1.0 -2.28 system 7.2.0 -2.29 system 7.3.0 -2.30 system 7.4.0 -2.31.1 system 8.1.0 -2.30 system 8.2.0 -2.31.1 system 8.3.0 -2.32 system 8.3.0 system 8.4.0 system 9.1.0 -2.32 system 9.2.0 -2.32 system 9.2.0 system 9.3.0 system 9.4.0 system 9.5.0 system system -2.29 system system system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GCCcore/","title":"GCCcore","text":"The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
homepage: https://gcc.gnu.org/
version toolchain 10.1.0 system 10.2.0 system 10.3.0 system 11.1.0 system 11.2.0 system 11.3.0 system 11.4.0 system 12.1.0 system 12.2.0 system 12.3.0 system 13.1.0 system 13.2.0 system 13.3.0 system 14.1.0 system 14.2.0 system 4.9.2 system 4.9.3 system 4.9.4 system 5.3.0 system 5.4.0 system 5.5.0 system 6.1.0 system 6.2.0 system 6.3.0 system 6.4.0 system 6.5.0 system 7.1.0 system 7.2.0 system 7.3.0 system 7.4.0 system 8.1.0 system 8.2.0 system 8.3.0 system 8.4.0 system 9.1.0 system 9.2.0 system 9.3.0 system 9.4.0 system 9.5.0 system system system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GCTA/","title":"GCTA","text":"GCTA (Genome-wide Complex Trait Analysis) is a software package, which was initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been extensively extended for many other analyses of data from genome-wide association studies (GWASs).
homepage: https://yanglab.westlake.edu.cn/software/gcta/
version toolchain 1.94.0beta foss/2021b 1.94.0beta gfbf/2022a 1.94.1 gfbf/2022a 1.94.1 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GConf/","title":"GConf","text":"GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage.
homepage: https://developer.gnome.org/gconf/
version toolchain 3.2.6 GCCcore/10.3.0 3.2.6 GCCcore/11.2.0 3.2.6 GCCcore/11.3.0 3.2.6 GCCcore/8.2.0 3.2.6 GCCcore/8.3.0 3.2.6 foss/2016a 3.2.6 foss/2018b 3.2.6 intel/2016a 3.2.6 intel/2016b 3.2.6 intel/2017a 3.2.6 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GD/","title":"GD","text":"GD.pm - Interface to Gd Graphics Library
homepage: https://github.com/lstein/Perl-GD
version versionsuffix toolchain 2.66 -Perl-5.24.0 foss/2016b 2.68 -Perl-5.26.1 GCCcore/6.4.0 2.69 -Perl-5.28.0 GCCcore/7.3.0 2.71 GCCcore/9.3.0 2.73 GCCcore/10.3.0 2.75 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GDAL/","title":"GDAL","text":"GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.
homepage: http://www.gdal.org/
version versionsuffix toolchain 2.0.2 foss/2016a 2.0.2 intel/2016a 2.1.0 foss/2016a 2.1.0 foss/2016b 2.1.0 intel/2016b 2.1.1 foss/2016a 2.1.1 -Python-2.7.12 intel/2016b 2.1.2 -Python-2.7.12 intel/2016b 2.1.3 -Python-2.7.12 foss/2016b 2.1.3 -Python-2.7.12 intel/2016b 2.1.3 -Python-2.7.13 intel/2017a 2.1.3 -Python-3.6.1 intel/2017a 2.2.0 -Python-2.7.13-HDF5-1.8.18 intel/2017a 2.2.0 -Python-2.7.13-HDF5-HDF intel/2017a 2.2.0 -Python-3.6.1 intel/2017a 2.2.2 -Python-2.7.14-HDF5-1.8.19 intel/2017b 2.2.2 -Python-2.7.14 intel/2017b 2.2.3 -Python-2.7.14 foss/2017b 2.2.3 -Python-3.6.3 foss/2017b 2.2.3 -Python-2.7.14 foss/2018a 2.2.3 -Python-3.6.4 foss/2018a 2.2.3 -Python-2.7.15 foss/2018b 2.2.3 -Python-3.6.6 foss/2018b 2.2.3 -Python-2.7.14 intel/2017b 2.2.3 -Python-2.7.14 intel/2018a 2.2.3 -Python-3.6.4 intel/2018a 2.2.3 -Python-3.6.6 intel/2018b 2.2.3 -Python-3.6.4 iomkl/2018a 2.4.4 foss/2021b 2.4.4 intel/2021b 3.0.0 -Python-2.7.15 foss/2019a 3.0.0 -Python-3.7.2 foss/2019a 3.0.0 -Python-2.7.15 intel/2019a 3.0.0 -Python-3.7.2 intel/2019a 3.0.2 -Python-3.7.4 foss/2019b 3.0.2 -Python-3.7.4 fosscuda/2019b 3.0.2 -Python-3.7.4 intel/2019b 3.0.4 -Python-3.8.2 foss/2020a 3.0.4 -Python-3.8.2 intel/2020a 3.2.1 foss/2020b 3.2.1 fosscuda/2020b 3.2.1 intel/2020b 3.3.0 foss/2021a 3.3.2 foss/2021b 3.5.0 foss/2022a 3.6.2 foss/2022b 3.7.1 foss/2023a 3.9.0 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GDB/","title":"GDB","text":"The GNU Project Debugger
homepage: https://www.gnu.org/software/gdb/gdb.html
version versionsuffix toolchain 10.1 GCCcore/10.2.0 10.2 GCCcore/10.3.0 10.2 -Python-3.8.2 GCCcore/9.3.0 11.1 GCCcore/11.2.0 12.1 GCCcore/11.3.0 13.2 GCCcore/12.2.0 13.2 GCCcore/12.3.0 13.2 GCCcore/13.2.0 14.2 GCCcore/13.3.0 7.10.1 -Python-2.7.11 foss/2016a 7.10.1 -Python-2.7.11 intel/2016a 7.11 -Python-2.7.11 foss/2016a 7.11 -Python-2.7.11 intel/2016a 7.11.1 -Python-2.7.12 foss/2016b 7.11.1 -Python-2.7.12 intel/2016b 7.8.2 GCC/4.9.2 7.9 GCC/4.9.2 8.0.1 -Python-2.7.14 foss/2017b 8.0.1 -Python-3.6.3 foss/2017b 8.1 -Python-2.7.14 foss/2018a 8.1.1 -Python-2.7.14 intel/2018a 8.3 -Python-3.7.2 GCCcore/8.2.0 9.1 -Python-3.7.4 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GDCHART/","title":"GDCHART","text":"Easy to use C API, high performance library to create charts and graphs in PNG, GIF and WBMP format.
homepage: http://users.fred.net/brv/chart
version toolchain 0.11.5dev GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GDCM/","title":"GDCM","text":"Grassroots DICOM: Cross-platform DICOM implementation
homepage: https://sourceforge.net/projects/gdcm
version toolchain 2.8.8 GCCcore/6.4.0 2.8.9 GCCcore/7.3.0 3.0.20 GCCcore/11.3.0 3.0.21 GCCcore/12.2.0 3.0.4 GCCcore/8.2.0 3.0.5 GCCcore/8.3.0 3.0.8 GCCcore/10.2.0 3.0.8 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GDGraph/","title":"GDGraph","text":"GDGraph is a Perl package to generate charts
homepage: https://metacpan.org/release/GDGraph
version versionsuffix toolchain 1.54 -Perl-5.28.0 foss/2018b 1.54 -Perl-5.26.1 intel/2018a 1.56 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GDMA/","title":"GDMA","text":"The GDMA program carries out Distributed Multipole Analysis of wavefunctions calculated by the Gaussian system of programs or the Psi4 package, using the formatted checkpoint files that they can produce. The result is a set of multipole moments at sites defined by the user (usually at the positions of the atomic nuclei) which, given an accurate wavefunction, provide an accurate description of the electrostatic field of the molecule.
homepage: https://gitlab.com/anthonyjs/gdma
version toolchain 2.3.3_20230603 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GDRCopy/","title":"GDRCopy","text":"A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology.
homepage: https://github.com/NVIDIA/gdrcopy
version versionsuffix toolchain 2.1 -CUDA-11.1.1 GCCcore/10.2.0 2.1 -CUDA-11.2.1 GCCcore/10.2.0 2.1 -CUDA-11.0.2 GCCcore/9.3.0 2.2 GCCcore/10.2.0 2.2 GCCcore/10.3.0 2.3 GCCcore/11.2.0 2.3 GCCcore/11.3.0 2.3 GCCcore/12.2.0 2.3.1 GCCcore/12.3.0 2.4 GCCcore/13.2.0 2.4.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GEGL/","title":"GEGL","text":"GEGL (Generic Graphics Library) is a data flow based image processing framework, providing floating point processing and non-destructive image processing capabilities to GNU Image Manipulation Program (GIMP) and other projects.
homepage: https://www.gegl.org
version toolchain 0.4.30 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GEM-library/","title":"GEM-library","text":"Next-generation sequencing platforms (Illumina/Solexa, ABI/SOLiD, etc.) call for powerful and very optimized tools to index/analyze huge genomes. The GEM library strives to be a true \"next-generation\" tool for handling any kind of sequence data, offering state-of-the-art algorithms and data structures specifically tailored to this demanding task. At the moment, efficient indexing and searching algorithms based on the Burrows-Wheeler transform (BWT) have been implemented. The library core is written in C for maximum speed, with concise interfaces to higher-level programming languages like OCaml and Python. Many high-performance standalone programs (mapper, splice mapper, etc.) are provided along with the library; in general, new algorithms and tools can be easily implemented on the top of it.
homepage: http://algorithms.cnag.cat/wiki/The_GEM_library
version versionsuffix toolchain 20130406-045632 _pre-release-3_Linux-x86_64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GEM/","title":"GEM","text":"GEM (Gene-Environment interaction analysis for Millions of samples) is a software program for large-scale gene-environment interaction testing in samples from unrelated individuals. It enables genome-wide association studies in up to millions of samples while allowing for multiple exposures, control for genotype-covariate interactions, and robust inference.
homepage: https://github.com/large-scale-gxe-methods/GEM
version toolchain 1.5.1 foss/2022a 1.5.1 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GEMMA/","title":"GEMMA","text":"Genome-wide Efficient Mixed Model Association
homepage: https://github.com/genetics-statistics/GEMMA
version toolchain 0.97 foss/2016b 0.97 foss/2017a 0.98.1 foss/2018b 0.98.5 foss/2020a 0.98.5 foss/2021b 0.98.5 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GEOS/","title":"GEOS","text":"GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
homepage: https://trac.osgeo.org/geos
version versionsuffix toolchain 3.10.3 GCC/11.3.0 3.11.1 GCC/12.2.0 3.12.0 GCC/12.3.0 3.12.1 GCC/13.2.0 3.5.0 -Python-2.7.11 intel/2016a 3.5.0 -Python-2.7.12 intel/2016b 3.6.1 -Python-2.7.12 foss/2016b 3.6.1 -Python-2.7.12 intel/2016b 3.6.1 -Python-2.7.13 intel/2017a 3.6.1 -Python-3.6.1 intel/2017a 3.6.2 -Python-2.7.14 foss/2017b 3.6.2 -Python-3.6.2 foss/2017b 3.6.2 -Python-3.6.3 foss/2017b 3.6.2 -Python-2.7.14 foss/2018a 3.6.2 -Python-3.6.4 foss/2018a 3.6.2 -Python-2.7.15 foss/2018b 3.6.2 -Python-3.6.6 foss/2018b 3.6.2 -Python-2.7.14 intel/2017b 3.6.2 -Python-3.6.3 intel/2017b 3.6.2 -Python-3.6.3 intel/2018.01 3.6.2 -Python-2.7.14 intel/2018a 3.6.2 -Python-3.6.4 intel/2018a 3.6.2 -Python-3.6.6 intel/2018b 3.6.2 -Python-3.6.4 iomkl/2018a 3.7.2 -Python-2.7.15 foss/2019a 3.7.2 -Python-3.7.2 foss/2019a 3.7.2 -Python-2.7.15 intel/2019a 3.7.2 -Python-3.7.2 intel/2019a 3.8.0 -Python-3.7.4 GCC/8.3.0 3.8.0 GCC/8.3.0 3.8.0 -Python-3.7.4 iccifort/2019.5.281 3.8.1 -Python-3.8.2 GCC/9.3.0 3.8.1 -Python-3.8.2 iccifort/2020.1.217 3.9.1 GCC/10.2.0 3.9.1 GCC/10.3.0 3.9.1 GCC/11.2.0 3.9.1 iccifort/2020.4.304 3.9.1 intel-compilers/2021.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GETORB/","title":"GETORB","text":"GETORB software package contains programs to handle the orbital data records (ODRs)
homepage: http://www.deos.tudelft.nl/ers/precorbs/tools/getorb_pack.shtml
version toolchain 2.3.2 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GFF3-toolkit/","title":"GFF3-toolkit","text":"Python programs for processing GFF3 files
homepage: https://gff3toolkit.readthedocs.io
version toolchain 2.1.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GFOLD/","title":"GFOLD","text":"Generalized fold change for ranking differentially expressed genes from RNA-seq data
homepage: http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html
version toolchain 1.1.4 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GHC/","title":"GHC","text":"The Glorious/Glasgow Haskell Compiler
homepage: http://haskell.org/ghc/
version versionsuffix toolchain 6.12.3 system 8.6.5 -x86_64 system 9.10.1 -x86_64 system 9.2.2 -x86_64 system 9.4.6 -x86_64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GI-DocGen/","title":"GI-DocGen","text":"GI-DocGen is a document generator for GObject-based libraries. GObject is the base type system of the GNOME project. GI-Docgen reuses the introspection data generated by GObject-based libraries to generate the API reference of these libraries, as well as other ancillary documentation.
homepage: https://gitlab.gnome.org/GNOME/gi-docgen
version toolchain 2023.3 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GIMIC/","title":"GIMIC","text":"The GIMIC program calculates magnetically induced currents in molecules. You need to provide this program with a density matrix in atomic-orbital (AO) basis and three (effective) magnetically perturbed AO density matrices in the proper format. Currently ACES2, Turbomole, G09, QChem, FERMION++, and LSDalton can produce these matrices.
homepage: https://gimic.readthedocs.io
version versionsuffix toolchain 2.2.1 foss/2022a 2018.04.20 -Python-2.7.14 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GIMP/","title":"GIMP","text":"GIMP is a cross-platform image editor available for GNU/Linux, OS X, Windows and more operating systems.
homepage: https://www.gimp.org
version toolchain 2.10.24 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GIMPS/","title":"GIMPS","text":"GIMPS: Great Internet Mersenne Prime Search; it can be useful for limited stress testing of nodes, in user space
homepage: http://www.mersenne.org/
version toolchain p95v279 GCC/4.8.2 p95v279.linux64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GKeyll/","title":"GKeyll","text":"Gkeyll v2.0 (pronounced as in the book \u201cThe Strange Case of Dr. Jekyll and Mr. Hyde\u201d) is a computational plasma physics code mostly written in C/C++ and LuaJIT. Gkeyll contains solvers for gyrokinetic equations, Vlasov-Maxwell equations, and multi-fluid equations. Gkeyll contains ab-initio and novel implementations of a number of algorithms, and perhaps is unique in using a JIT compiled typeless dynamic language for as its main implementation language.
homepage: https://gkeyll.readthedocs.io
version versionsuffix toolchain 20220803 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GKlib-METIS/","title":"GKlib-METIS","text":"A library of various helper routines and frameworks used by many of the lab's software
homepage: https://github.com/KarypisLab/GKlib
version toolchain 5.1.1 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GL2PS/","title":"GL2PS","text":"GL2PS: an OpenGL to PostScript printing library
homepage: http://www.geuz.org/gl2ps/
version versionsuffix toolchain 1.3.9 -Mesa-11.2.1 foss/2016a 1.3.9 foss/2016a 1.3.9 foss/2016b 1.3.9 -Mesa-11.2.1 intel/2016a 1.3.9 intel/2016a 1.3.9 intel/2016b 1.4.0 GCCcore/8.3.0 1.4.0 foss/2017b 1.4.0 foss/2018a 1.4.0 foss/2018b 1.4.0 foss/2019a 1.4.0 intel/2017a 1.4.0 intel/2017b 1.4.0 intel/2018a 1.4.2 GCCcore/10.2.0 1.4.2 GCCcore/10.3.0 1.4.2 GCCcore/11.2.0 1.4.2 GCCcore/11.3.0 1.4.2 GCCcore/12.2.0 1.4.2 GCCcore/12.3.0 1.4.2 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GLFW/","title":"GLFW","text":"GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop
homepage: https://www.glfw.org
version toolchain 3.2.1 intel/2018a 3.3.2 GCCcore/9.3.0 3.3.3 GCCcore/10.2.0 3.3.4 GCCcore/10.3.0 3.3.4 GCCcore/11.2.0 3.3.8 GCCcore/11.3.0 3.4 GCCcore/12.2.0 3.4 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GLI/","title":"GLI","text":"Graphics Language Interpreter
homepage: https://pgi-jcns.fz-juelich.de/portal/pages/gli.html
version toolchain 4.5.31 GCCcore/10.2.0 4.5.31 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GLIMMER/","title":"GLIMMER","text":"Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
homepage: http://ccb.jhu.edu/software/glimmer/index.shtml
version toolchain 3.02b foss/2016b 3.02b foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GLIMPSE/","title":"GLIMPSE","text":"GLIMPSE2 is a set of tools for phasing and imputation for low-coverage sequencing datasets
homepage: https://github.com/odelaneau/GLIMPSE
version toolchain 2.0.0 GCC/10.3.0 2.0.0 GCC/11.3.0 2.0.0 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GLM-AED/","title":"GLM-AED","text":"The General Lake Model (GLM) is a water balance and one-dimensional vertical stratification hydrodynamic model, which is dynamically coupled with the AED water quality modelling library. GLM-AED is suitable for simulating conditions in a wide range of natural and engineered lakes, including shallow (well-mixed) and deep (stratified) systems. The model has been successfully applied to systems from the scale of individual ponds and wetlands, to actively operated reservoirs, upto the scale of the Great Lakes.
homepage: https://github.com/AquaticEcoDynamics/glm-aed
version toolchain 3.3.0a5 gompi/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GLM/","title":"GLM","text":"OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.
homepage: https://github.com/g-truc/glm
version toolchain 0.9.7.6 intel/2016a 0.9.8.3 GCCcore/5.4.0 0.9.8.3 GCCcore/7.3.0 0.9.9.0 GCCcore/6.4.0 0.9.9.8 GCCcore/10.2.0 0.9.9.8 GCCcore/10.3.0 0.9.9.8 GCCcore/11.2.0 0.9.9.8 GCCcore/11.3.0 0.9.9.8 GCCcore/12.2.0 0.9.9.8 GCCcore/12.3.0 0.9.9.8 GCCcore/8.3.0 1.0.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GLPK/","title":"GLPK","text":"The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
homepage: https://www.gnu.org/software/glpk/
version toolchain 4.58 foss/2016a 4.58 intel/2016a 4.60 GCCcore/5.4.0 4.60 intel/2016b 4.61 intel/2017a 4.65 GCCcore/10.2.0 4.65 GCCcore/6.4.0 4.65 GCCcore/7.3.0 4.65 GCCcore/8.2.0 4.65 GCCcore/8.3.0 4.65 GCCcore/9.3.0 5.0 GCCcore/10.3.0 5.0 GCCcore/11.2.0 5.0 GCCcore/11.3.0 5.0 GCCcore/12.2.0 5.0 GCCcore/12.3.0 5.0 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GLib/","title":"GLib","text":"GLib is one of the base libraries of the GTK+ project
homepage: http://www.gtk.org/
version toolchain 2.42.1 GCC/4.9.2 2.44.0 GCC/4.9.2 2.47.5 foss/2016a 2.47.5 gimkl/2.11.5 2.47.5 intel/2016a 2.48.0 foss/2016a 2.48.0 intel/2016a 2.49.5 foss/2016b 2.49.5 intel/2016b 2.52.0 foss/2017a 2.52.0 intel/2017a 2.53.5 GCCcore/6.3.0 2.53.5 GCCcore/6.4.0 2.54.2 GCCcore/6.4.0 2.54.3 GCCcore/6.4.0 2.54.3 GCCcore/7.3.0 2.60.1 GCCcore/8.2.0 2.62.0 GCCcore/8.3.0 2.64.1 GCCcore/9.3.0 2.66.1 GCCcore/10.2.0 2.68.2 GCCcore/10.3.0 2.69.1 GCCcore/11.2.0 2.72.1 GCCcore/11.3.0 2.75.0 GCCcore/12.2.0 2.77.1 GCCcore/12.3.0 2.78.1 GCCcore/13.2.0 2.80.4 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GLibmm/","title":"GLibmm","text":"C++ bindings for Glib
homepage: https://www.gtk.org/
version toolchain 2.49.7 GCCcore/7.3.0 2.49.7 GCCcore/8.2.0 2.49.7 GCCcore/8.3.0 2.66.4 GCCcore/10.3.0 2.72.1 GCCcore/11.3.0 2.75.0 GCCcore/12.2.0 2.77.0 GCCcore/12.3.0 2.78.1 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GMAP-GSNAP/","title":"GMAP-GSNAP","text":"GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program
homepage: http://research-pub.gene.com/gmap/
version toolchain 2016-05-01 foss/2016a 2016-11-07 foss/2016b 2018-05-11 intel/2018a 2018-07-04 intel/2018a 2019-03-15 foss/2018b 2019-09-12 GCC/8.3.0 2020-12-17 GCC/9.3.0 2021-12-17 GCC/11.2.0 2023-02-17 GCC/11.3.0 2023-04-20 GCC/10.3.0 2023-04-20 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GMP-ECM/","title":"GMP-ECM","text":"Yet another implementation of the Elliptic Curve Method.
homepage: https://gitlab.inria.fr/zimmerma/ecm
version toolchain 7.0.5 GCCcore/11.3.0 7.0.5 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GMP/","title":"GMP","text":"GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
homepage: http://gmplib.org/
version toolchain 4.3.2 system 5.1.3 GCC/4.8.2 6.0.0 GCC/4.9.2 6.0.0a GCC/4.8.4 6.0.0a GCC/4.9.2 6.0.0a GNU/4.9.3-2.25 6.1.0 GCC/4.9.3-2.25 6.1.0 foss/2016a 6.1.0 gimkl/2.11.5 6.1.0 intel/2016.02-GCC-4.9 6.1.0 intel/2016a 6.1.0 iomkl/2016.07 6.1.0 iomkl/2016.09-GCC-4.9.3-2.25 6.1.1 GCC/5.4.0-2.26 6.1.1 GCCcore/5.4.0 6.1.1 GCCcore/6.3.0 6.1.1 foss/2016.04 6.1.1 foss/2016a 6.1.1 foss/2016b 6.1.1 intel/2016b 6.1.2 GCCcore/6.3.0 6.1.2 GCCcore/6.4.0 6.1.2 GCCcore/7.3.0 6.1.2 GCCcore/8.2.0 6.1.2 GCCcore/8.3.0 6.1.2 foss/2016b 6.2.0 GCCcore/10.2.0 6.2.0 GCCcore/9.3.0 6.2.1 GCCcore/10.3.0 6.2.1 GCCcore/11.2.0 6.2.1 GCCcore/11.3.0 6.2.1 GCCcore/12.2.0 6.2.1 GCCcore/12.3.0 6.3.0 GCCcore/13.2.0 6.3.0 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GMT/","title":"GMT","text":"GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools.
homepage: http://gmt.soest.hawaii.edu/
version toolchain 4.5.17 foss/2018a 5.4.1 intel/2017a 5.4.3 foss/2018a 5.4.3 intel/2017b 5.4.5 foss/2019a 6.2.0 foss/2019b 6.2.0 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GNU/","title":"GNU","text":"Compiler-only toolchain with GCC and binutils.
homepage: http://www.gnu.org/software/
version toolchain 4.9.2-2.25 system 4.9.3-2.25 system 5.1.0-2.25 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GOATOOLS/","title":"GOATOOLS","text":"A Python library for Gene Ontology analyses
homepage: https://github.com/tanghaibao/goatools
version toolchain 1.1.6 foss/2020b 1.3.1 foss/2021b 1.3.1 foss/2022a 1.4.5 foss/2022b 1.4.5 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GOBNILP/","title":"GOBNILP","text":"GOBNILP (Globally Optimal Bayesian Network learning using Integer Linear Programming) is a C program which learns Bayesian networks from complete discrete data or from local scores.
homepage: https://www.cs.york.ac.uk/aig/sw/gobnilp/
version toolchain 1.6.3 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GOMC/","title":"GOMC","text":"GPU Optimized Monte Carlo (GOMC) is a parallel molecular simulation code designed for high-performance simulation of large systems.
homepage: https://gomc-wsu.org/
version versionsuffix toolchain 2.76-20230613 -CUDA-11.7.0 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GObject-Introspection/","title":"GObject-Introspection","text":"GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.
homepage: https://wiki.gnome.org/GObjectIntrospection/
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","boost":0.5},{"location":"version-specific/supported-software/g/GP2C/","title":"GP2C","text":"The gp2c compiler is a package for translating GP routines into the C programming language, so that they can be compiled and used with the PARI system or the GP calculator.
homepage: http://pari.math.u-bordeaux.fr/pub/pari/manuals/gp2c/gp2c.html
version toolchain 0.0.9pl5 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GPAW-setups/","title":"GPAW-setups","text":"PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed.
homepage: https://wiki.fysik.dtu.dk/gpaw/
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","boost":0.5},{"location":"version-specific/supported-software/g/GPAW/","title":"GPAW","text":"GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions.
homepage: https://wiki.fysik.dtu.dk/gpaw/
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","boost":0.5},{"location":"version-specific/supported-software/g/GPflow/","title":"GPflow","text":"GPflow is a package for building Gaussian process models in Python. It implements modern Gaussian process inference for composable kernels and likelihoods.
homepage: https://gpflow.github.io
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","boost":0.5},{"location":"version-specific/supported-software/g/GPy/","title":"GPy","text":"GPy is a Gaussian Process (GP) framework written in Python
homepage: https://sheffieldml.github.io/GPy
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","boost":0.5},{"location":"version-specific/supported-software/g/GPyOpt/","title":"GPyOpt","text":"GPyOpt is a Python open-source library for Bayesian Optimization
homepage: https://sheffieldml.github.io/GPyOpt
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","boost":0.5},{"location":"version-specific/supported-software/g/GPyTorch/","title":"GPyTorch","text":"GPyTorch is a Gaussian process library implemented using PyTorch.
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","boost":0.5},{"location":"version-specific/supported-software/g/GRASP-suite/","title":"GRASP-suite","text":"GRASP-suite is a collection of tools and tutorials to perform and analyse ancestral sequence reconstruction.
homepage: https://github.com/bodenlab/GRASP-suite/
version versionsuffix toolchain 2023-05-09 -Java-17 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GRASP/","title":"GRASP","text":"The General Relativistic Atomic Structure Package (GRASP) is a set of Fortran 90 programs for performing fully-relativistic electron structure calculations of atoms.
homepage: https://compas.github.io/grasp/
version toolchain 2018 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GRASS/","title":"GRASS","text":"The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization
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version versionsuffix toolchain 7.6.0 -Python-2.7.15 foss/2018b 7.8.3 -Python-3.7.4 fosscuda/2019b 8.2.0 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GRIDSS/","title":"GRIDSS","text":"GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.
homepage: https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation
version versionsuffix toolchain 2.13.2 -Java-11 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GRIT/","title":"GRIT","text":"GRIT - A tool for the integrative analysis of RNA-seq type assays
homepage: https://github.com/nboley/grit
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","boost":0.5},{"location":"version-specific/supported-software/g/GRNBoost/","title":"GRNBoost","text":"XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable.
homepage: https://github.com/dmlc/xgboost
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","boost":0.5},{"location":"version-specific/supported-software/g/GROMACS/","title":"GROMACS","text":"GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
homepage: http://www.gromacs.org
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","boost":0.5},{"location":"version-specific/supported-software/g/GSD/","title":"GSD","text":"The GSD file format is the native file format for HOOMD-blue. GSD files store trajectories of the HOOMD-blue system state in a binary file with efficient random access to frames. GSD allows all particle and topology properties to vary from one frame to the next. Use the GSD Python API to specify the initial condition for a HOOMD-blue simulation or analyze trajectory output with a script. Read a GSD trajectory with a visualization tool to explore the behavior of the simulation.
homepage: https://gsd.readthedocs.io
version toolchain 3.2.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GSEA/","title":"GSEA","text":"Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).
homepage: https://www.gsea-msigdb.org/gsea/index.jsp
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","boost":0.5},{"location":"version-specific/supported-software/g/GSL/","title":"GSL","text":"The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
homepage: http://www.gnu.org/software/gsl/
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homepage: https://gstreamer.freedesktop.org/
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","boost":0.5},{"location":"version-specific/supported-software/g/GStreamer/","title":"GStreamer","text":"GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.
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","boost":0.5},{"location":"version-specific/supported-software/g/GTDB-Tk/","title":"GTDB-Tk","text":"A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
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","boost":0.5},{"location":"version-specific/supported-software/g/GTK%2B/","title":"GTK+","text":"The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
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","boost":0.5},{"location":"version-specific/supported-software/g/GTK2/","title":"GTK2","text":"The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
homepage: https://developer.gnome.org/gtk+/stable/
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","boost":0.5},{"location":"version-specific/supported-software/g/GTK3/","title":"GTK3","text":"GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction.
homepage: https://developer.gnome.org/gtk3/stable/
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","boost":0.5},{"location":"version-specific/supported-software/g/GTK4/","title":"GTK4","text":"GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction.
homepage: https://docs.gtk.org/gtk4/
version toolchain 4.11.3 GCC/12.2.0 4.13.1 GCC/12.3.0 4.7.0 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GTOOL/","title":"GTOOL","text":"GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.
homepage: http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html
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","boost":0.5},{"location":"version-specific/supported-software/g/GTS/","title":"GTS","text":"GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles.
homepage: http://gts.sourceforge.net/
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","boost":0.5},{"location":"version-specific/supported-software/g/GUIDANCE/","title":"GUIDANCE","text":"GUIDANCE is a software package for aligning biological sequences (DNA or amino acids) using either MAFFT, PRANK, or CLUSTALW, and calculating confidence scores for each column, sequence and residue in the alignment.
homepage: https://taux.evolseq.net/guidance/
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","boost":0.5},{"location":"version-specific/supported-software/g/GULP/","title":"GULP","text":"GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids)Band Unfolding code for Plane-wave based calculations
homepage: https://gulp.curtin.edu.au/gulp/
version toolchain 5.1 intel/2019a 6.1 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GUSHR/","title":"GUSHR","text":"Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation.
homepage: https://github.com/Gaius-Augustus/GUSHR
version toolchain 2020-09-28 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Gaia/","title":"Gaia","text":"Gaia is a C++ library with python bindings which implements similarity measures and classi\ufb01cations on the results of audio analysis, and generates classi\ufb01cation models that Essentia can use to compute high-level description of music.
homepage: https://github.com/MTG/gaia
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homepage: https://sourceforge.net/projects/soapdenovo2/files/GapCloser/
version toolchain 1.12-r6 foss/2018a 1.12-r6 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GapFiller/","title":"GapFiller","text":"GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data.
homepage: https://sourceforge.net/projects/gapfiller
version toolchain 2.1.1 intel/2017a 2.1.2 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Gaussian/","title":"Gaussian","text":"Gaussian provides state-of-the-art capabilities for electronic structure modeling. Gaussian 09 is licensed for a wide variety of computer systems. All versions of Gaussian 09 contain every scientific/modeling feature, and none imposes any artificial limitations on calculations other than your computing resources and patience. This is the official gaussian AVX build.
homepage: https://www.gaussian.com/
version versionsuffix toolchain 09.e.01 -AVX system 16.A.03 -AVX2 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Gblocks/","title":"Gblocks","text":"Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
homepage: https://www.biologiaevolutiva.org/jcastresana/Gblocks.html
version toolchain 0.91b system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Gctf/","title":"Gctf","text":"Gctf: real-time CTF determination and correction, Kai Zhang, 2016
homepage: https://www.mrc-lmb.cam.ac.uk/kzhang/
version toolchain 1.06 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Gdk-Pixbuf/","title":"Gdk-Pixbuf","text":"The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.
homepage: https://developer.gnome.org/gdk-pixbuf/stable/
version toolchain 2.32.3 intel/2016a 2.35.1 foss/2016a 2.35.1 intel/2016a 2.36.0 foss/2016b 2.36.0 intel/2016b 2.36.10 intel/2017a 2.36.11 foss/2017b 2.36.11 foss/2018a 2.36.11 fosscuda/2018b 2.36.11 intel/2017b 2.36.11 intel/2018a 2.36.12 foss/2018b 2.36.12 fosscuda/2018b 2.36.8 intel/2017a 2.38.1 GCCcore/8.2.0 2.38.2 GCCcore/8.3.0 2.40.0 GCCcore/10.2.0 2.40.0 GCCcore/9.3.0 2.42.10 GCCcore/12.2.0 2.42.10 GCCcore/12.3.0 2.42.10 GCCcore/13.2.0 2.42.11 GCCcore/13.3.0 2.42.6 GCCcore/10.3.0 2.42.6 GCCcore/11.2.0 2.42.8 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Gdspy/","title":"Gdspy","text":"Gdspy is a Python module for creation and manipulation of GDSII stream files.
homepage: https://github.com/heitzmann/gdspy
version toolchain 1.6.13 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Geant4-data/","title":"Geant4-data","text":"Datasets for Geant4.
homepage: https://geant4.web.cern.ch/
version toolchain 11.1 system 11.2 system 20201103 system 20210510 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Geant4/","title":"Geant4","text":"Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
homepage: https://geant4.cern.ch
version toolchain 10.01.p03 intel/2016a 10.02.p01 intel/2016a 10.03.p03 foss/2017b 10.03.p03 intel/2017b 10.04 intel/2017b 10.5 foss/2017b 10.5 foss/2018b 10.5 intel/2017b 10.5 intel/2018b 10.6 foss/2019b 10.6.2 foss/2020a 10.7.1 GCC/10.2.0 10.7.1 GCC/11.2.0 11.0.0 GCC/11.2.0 11.0.1 GCC/11.2.0 11.0.2 GCC/11.2.0 11.0.2 GCC/11.3.0 11.1.2 GCC/11.3.0 11.2.2 GCC/12.3.0 9.5.p02 intel/2016a 9.6.p04 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GenMap/","title":"GenMap","text":"GenMap - Fast and Exact Computation of Genome Mappability
homepage: https://github.com/cpockrandt/genmap
version toolchain 1.3.0 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GeneMark-ET/","title":"GeneMark-ET","text":"Eukaryotic gene prediction suite with automatic training
homepage: http://exon.gatech.edu/GeneMark
version toolchain 4.38 GCCcore/8.2.0 4.57 GCCcore/8.3.0 4.65 GCCcore/10.2.0 4.71 GCCcore/11.2.0 4.71 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GenerativeModels/","title":"GenerativeModels","text":"homepage: https://monai.io/
version versionsuffix toolchain 0.2.1 -CUDA-11.7.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GenomeComb/","title":"GenomeComb","text":"Genomecomb is a package designed to analyze, combine, annotate and query genome as well as transcriptome sequencing data.
homepage: https://github.com/derijkp/genomecomb
version versionsuffix toolchain 0.106.0 -x86_64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GenomeMapper/","title":"GenomeMapper","text":"GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. This version is used to align against a single reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use this one.
homepage: https://1001genomes.org/software/genomemapper_singleref.html
version toolchain 0.4.4 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GenomeTester4/","title":"GenomeTester4","text":"A toolkit for performing set operations - union, intersection and complement - on k-mer lists.
homepage: https://github.com/bioinfo-ut/GenomeTester4
version toolchain 4.0 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GenomeThreader/","title":"GenomeThreader","text":"GenomeThreader is a software tool to compute gene structure predictions.
homepage: http://genomethreader.org
version versionsuffix toolchain 1.7.1 -Linux_x86_64-64bit system 1.7.3 -Linux_x86_64-64bit system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GenomeTools/","title":"GenomeTools","text":"A comprehensive software library for efficient processing of structured genome annotations.
homepage: http://genometools.org
version versionsuffix toolchain 1.5.10 -Python-2.7.15 foss/2018b 1.5.10 foss/2018b 1.6.1 GCC/10.2.0 1.6.1 -Python-2.7.16 GCC/8.3.0 1.6.1 GCC/8.3.0 1.6.1 GCC/9.3.0 1.6.2 GCC/10.3.0 1.6.2 GCC/11.3.0 1.6.2 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GenomeWorks/","title":"GenomeWorks","text":"SDK for GPU accelerated genome assembly and analysis
homepage: https://github.com/clara-parabricks/GenomeWorks
version toolchain 2021.02.2 fosscuda/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Genome_Profiler/","title":"Genome_Profiler","text":"Genome Profiler (GeP) is a program to perform whole-genome multilocus sequence typing (wgMLST) analysis for bacterial isolates
homepage: https://sourceforge.net/projects/genomeprofiler/
version versionsuffix toolchain 2.1 -Perl-5.24.0 foss/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GenotypeHarmonizer/","title":"GenotypeHarmonizer","text":"The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.
homepage: https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer
version versionsuffix toolchain 1.4.14 -Java-1.7.0_80 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GeoDict/","title":"GeoDict","text":"The innovative and easy-to-use material simulator GeoDict is the most complete software solution for multi-scale 3D image processing, modeling of materials, visualization, material property characterization, simulation-based material development, and optimization of processes.
homepage: https://www.math2market.com/geodict-software/geodict-applications.html
version toolchain 2024.SP2 gmpich/2024.06 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Gerris/","title":"Gerris","text":"Gerris is a Free Software program for the solution of the partial differential equations describing fluid flow
homepage: http://gfs.sourceforge.net/wiki/index.php/Main_Page
version toolchain 20131206 foss/2017b 20131206 gompi/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GetOrganelle/","title":"GetOrganelle","text":"This toolkit assemblies organelle genome from genomic skimming data.
homepage: https://github.com/Kinggerm/GetOrganelle
version versionsuffix toolchain 1.7.2 -Python-3.8.2 foss/2020a 1.7.4-pre2 foss/2020b 1.7.5.3 foss/2021b 1.7.6.1 foss/2021b 1.7.7.0 foss/2022a 1.7.7.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GffCompare/","title":"GffCompare","text":"GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files.
homepage: https://github.com/gpertea/gffcompare
version toolchain 0.10.1 foss/2016b 0.10.6 GCCcore/7.3.0 0.11.6 GCCcore/8.3.0 0.11.6 GCCcore/9.3.0 0.12.2 GCC/10.3.0 0.12.6 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Ghostscript/","title":"Ghostscript","text":"Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.
homepage: https://ghostscript.com
version versionsuffix toolchain 10.0.0 GCCcore/12.2.0 10.01.2 GCCcore/12.3.0 10.02.1 GCCcore/13.2.0 10.03.1 GCCcore/13.3.0 9.19 intel/2016a 9.19 intel/2016b 9.20 foss/2016b 9.20 intel/2016b 9.21 intel/2017a 9.22 -cairo-1.14.12 GCCcore/6.4.0 9.22 GCCcore/6.4.0 9.22 foss/2017b 9.22 intel/2017b 9.23 -cairo-1.14.12 GCCcore/6.4.0 9.23 GCCcore/6.4.0 9.23 GCCcore/7.3.0 9.27 GCCcore/8.2.0 9.50 GCCcore/8.3.0 9.52 GCCcore/9.3.0 9.53.3 GCCcore/10.2.0 9.54.0 GCCcore/10.3.0 9.54.0 GCCcore/11.2.0 9.56.1 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Gibbs2/","title":"Gibbs2","text":"Gibbs2 is a program for the calculation of thermodynamic properties in periodic solids under arbitrary conditions of temperature and pressure. Gibbs2 uses the results of periodic solid-state quantum-mechanical calculations, specifically the energy-volume curve and possibly the harmonic phonon frequencies, to compute the thermodynamic properties of the solid within the framework of the quasiharmonic approximation.
homepage: https://aoterodelaroza.github.io/gibbs2/
version toolchain 1.0 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GimmeMotifs/","title":"GimmeMotifs","text":"Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments
homepage: https://github.com/vanheeringen-lab/gimmemotifs
version toolchain 0.17.2 foss/2022a 0.17.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Giotto-Suite/","title":"Giotto-Suite","text":"Giotto Suite is focused on building a modular platform for analyzing spatial-omics technologies and strives to be interoperable with other popular spatial analysis tools and classes. Using established packages optimized for large(r) data, Giotto Suite adopts fast and memory efficient methods to create an interactive analysis.
homepage: https://github.com/drieslab/Giotto
version versionsuffix toolchain 3.0.1 -R-4.2.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GitPython/","title":"GitPython","text":"GitPython is a python library used to interact with Git repositories
homepage: https://github.com/gitpython-developers/GitPython
version versionsuffix toolchain 2.1.11 -Python-3.6.6 foss/2018b 2.1.11 -Python-3.6.6 intel/2018b 2.1.15 system 3.0.3 -Python-3.7.2 GCCcore/8.2.0 3.1.0 -Python-3.7.4 GCCcore/8.3.0 3.1.14 GCCcore/10.2.0 3.1.18 GCCcore/10.3.0 3.1.24 GCCcore/11.2.0 3.1.27 GCCcore/11.3.0 3.1.31 GCCcore/12.2.0 3.1.40 GCCcore/12.3.0 3.1.42 GCCcore/13.2.0 3.1.43 GCCcore/13.3.0 3.1.9 -Python-3.8.2 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Givaro/","title":"Givaro","text":"C++ library for arithmetic and algebraic computations
homepage: http://givaro.forge.imag.fr/
version toolchain 4.0.1 foss/2016a 4.2.0 GCCcore/11.3.0 4.2.0 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Giza/","title":"Giza","text":"Giza is an open, lightweight scientific plotting library built on top of cairo that provides uniform output to multiple devices.
homepage: https://danieljprice.github.io/giza/
version toolchain 1.1.0 foss/2018b 1.4.1 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Glade/","title":"Glade","text":"Glade is a RAD tool to enable quick & easy development of user interfaces for the GTK+ toolkit and the GNOME desktop environment.
homepage: https://glade.gnome.org/
version versionsuffix toolchain 3.8.5 -Python-2.7.11 intel/2016a 3.8.5 -Python-2.7.14 intel/2017b 3.8.6 -Python-2.7.15 foss/2018b 3.8.6 -Python-2.7.14 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GlimmerHMM/","title":"GlimmerHMM","text":"GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.
homepage: https://ccb.jhu.edu/software/glimmerhmm
version toolchain 3.0.4 foss/2016b 3.0.4 foss/2018b 3.0.4c GCC/10.2.0 3.0.4c GCC/11.2.0 3.0.4c GCC/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GlobalArrays/","title":"GlobalArrays","text":"Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model
homepage: http://hpc.pnl.gov/globalarrays
version versionsuffix toolchain 5.7 intel/2018b 5.7 -peigs intel/2019a 5.7.2 -peigs intel/2019b 5.7.2 intel/2019b 5.8 intel/2020a 5.8 intel/2021a 5.8 iomkl/2021a 5.8.1 intel/2022a 5.8.2 intel/2022a 5.8.2 intel/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Globus-CLI/","title":"Globus-CLI","text":"A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases.
homepage: https://docs.globus.org/cli/
version toolchain 1.11.0 GCCcore/8.3.0 3.1.1 GCCcore/10.2.0 3.2.0 GCCcore/10.3.0 3.6.0 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GlobusConnectPersonal/","title":"GlobusConnectPersonal","text":"Globus Connect Personal turns your laptop or other personal computer into a Globus endpoint with a just a few clicks. With Globus Connect Personal you can share and transfer files to/from a local machine\u2014campus server, desktop computer or laptop\u2014even if it's behind a firewall and you don't have administrator privileges.
homepage: https://www.globus.org/globus-connect-personal
version toolchain 2.3.6 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Glucose/","title":"Glucose","text":"Glucose is based on a new scoring scheme (well, not so new now, it was introduced in 2009) for the clause learning mechanism of so called Modern SAT solvers (it is based on our IJCAI'09 paper). It is designed to be parallel, since v4.0.
homepage: https://www.labri.fr/perso/lsimon/glucose/
version toolchain 4.1 GCC/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GnuTLS/","title":"GnuTLS","text":"GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability.
homepage: http://www.gnutls.org/
version toolchain 3.3.21 intel/2016a 3.4.11 foss/2016a 3.4.7 GNU/4.9.3-2.25 3.7.2 GCCcore/10.3.0 3.7.3 GCCcore/11.2.0 3.7.8 GCCcore/11.3.0 3.7.8 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Go/","title":"Go","text":"Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
homepage: https://www.golang.org
version toolchain 1.11.5 system 1.12.1 GCCcore/7.3.0 1.12 system 1.13.1 system 1.14.1 system 1.14 system 1.16.3 system 1.16.5 system 1.16.6 system 1.17.3 system 1.17.6 system 1.18.1 system 1.18.3 system 1.2.1 GCC/4.8.2 1.20.4 system 1.21.1 system 1.21.2 system 1.21.6 system 1.22.1 system 1.4.2 GCC/4.8.4 1.5 GCC/4.8.4 1.8.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Godon/","title":"Godon","text":"Godon is codon models software written in Go.
homepage: https://bitbucket.org/Davydov/godon/
version versionsuffix toolchain 20210913 -x86_64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GraPhlAn/","title":"GraPhlAn","text":"GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
homepage: https://segatalab.github.io/tools/graphlan
version versionsuffix toolchain 1.1.3 -Python-2.7.16 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Grace/","title":"Grace","text":"Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.
homepage: https://plasma-gate.weizmann.ac.il/Grace/
version versionsuffix toolchain 5.1.25 foss/2016a 5.1.25 -5build1 foss/2017b 5.1.25 -5build1 foss/2018a 5.1.25 -5build1 foss/2019a 5.1.25 -5build1 foss/2019b 5.1.25 foss/2021a 5.1.25 foss/2021b 5.1.25 intel/2016a 5.1.25 -5build1 intel/2017b 5.1.25 -5build1 intel/2019a 5.1.25 -5build1 intel/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Gradle/","title":"Gradle","text":"Complete Gradle install. From mobile apps to microservices, from small startups to big enterprises, Gradle helps teams build, automate and deliver better software, faster.
homepage: https://gradle.org
version versionsuffix toolchain 4.5.1 system 6.1.1 system 6.9.1 system 8.6 -Java-17 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GraphDB/","title":"GraphDB","text":"GraphDB is an enterprise ready Semantic Graph Database, compliant with W3C Standards. Semantic graph databases (also called RDF triplestores) provide the core infrastructure for solutions where modelling agility, data integration, relationship exploration and cross-enterprise data publishing and consumption are important.
homepage: https://graphdb.ontotext.com/
version toolchain 10.1.5 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GraphMap/","title":"GraphMap","text":"A highly sensitive and accurate mapper for long, error-prone reads
homepage: https://github.com/isovic/graphmap
version toolchain 0.5.2 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GraphMap2/","title":"GraphMap2","text":"A highly sensitive and accurate mapper for long, error-prone reads
homepage: https://github.com/lbcb-sci/graphmap2
version toolchain 0.6.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Graphene/","title":"Graphene","text":"Graphene is a thin layer of types for graphic libraries
homepage: https://ebassi.github.io/graphene/
version toolchain 1.10.8 GCCcore/11.3.0 1.10.8 GCCcore/12.2.0 1.10.8 GCCcore/12.3.0 1.10.8 GCCcore/13.2.0 1.6.0 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GraphicsMagick/","title":"GraphicsMagick","text":"GraphicsMagick is the swiss army knife of image processing.
homepage: http://www.graphicsmagick.org/
version toolchain 1.3.23 foss/2016a 1.3.23 intel/2016a 1.3.25 intel/2016b 1.3.25 intel/2017a 1.3.28 foss/2018a 1.3.31 foss/2018b 1.3.34 foss/2019a 1.3.34 foss/2019b 1.3.36 GCCcore/11.2.0 1.3.36 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Graphviz/","title":"Graphviz","text":"Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.
homepage: http://www.graphviz.org/
version versionsuffix toolchain 2.38.0 foss/2016b 2.38.0 intel/2016b 2.40.1 -Python-2.7.15 foss/2018b 2.40.1 foss/2018b 2.40.1 intel/2018a 2.42.2 -Java-11 GCCcore/8.3.0 2.42.2 -Python-3.7.4 foss/2019b 2.42.2 foss/2019b 2.44.1 -Java-11-Python-3.8.2 GCCcore/9.3.0 2.44.1 -Java-11 GCCcore/9.3.0 2.47.0 -Java-11 GCCcore/10.2.0 2.47.2 GCCcore/10.3.0 2.50.0 GCCcore/11.2.0 5.0.0 GCCcore/11.3.0 8.1.0 GCCcore/12.2.0 8.1.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Greenlet/","title":"Greenlet","text":"The greenlet package is a spin-off of Stackless, a version of CPython that supports micro-threads called \"tasklets\". Tasklets run pseudo-concurrently (typically in a single or a few OS-level threads) and are synchronized with data exchanges on \"channels\". A \"greenlet\", on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs.
homepage: https://github.com/python-greenlet/greenlet
version versionsuffix toolchain 0.4.11 -Python-2.7.12 intel/2016b 0.4.12 -Python-2.7.14 intel/2017b 0.4.9 -Python-2.7.11 intel/2016a 0.4.9 -Python-3.5.1 intel/2016a 2.0.2 GCCcore/11.3.0 2.0.2 GCCcore/12.2.0 2.0.2 GCCcore/12.3.0 3.0.2 GCCcore/12.3.0 3.0.3 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Grep/","title":"Grep","text":"The grep command searches one or more input files for lines containing a match to a specified pattern. By default, grep prints the matching lines.
homepage: http://www.gnu.org/software/grep/
version toolchain 2.21 GCC/4.9.2 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GroIMP/","title":"GroIMP","text":"GroIMP (Growth Grammar-related Interactive Modelling Platform) is a 3D-modelling platform.
homepage: http://www.grogra.de/software/groimp
version toolchain 1.5 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GromacsWrapper/","title":"GromacsWrapper","text":"GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools into python scripts.
homepage: https://gromacswrapper.readthedocs.org
version versionsuffix toolchain 0.8.0 -Python-3.7.2 fosscuda/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Groovy/","title":"Groovy","text":"Groovy is a powerful, optionally typed and dynamic language, with static-typing and static compilation capabilities, for the Java platform aimed at improving developer productivity thanks to a concise, familiar and easy to learn syntax.
homepage: https://groovy-lang.org
version versionsuffix toolchain 2.5.9 -Java-11 system 4.0.3 -Java-11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/GtkSourceView/","title":"GtkSourceView","text":"GtkSourceView is a GNOME library that extends GtkTextView, the standard GTK+ widget for multiline text editing. GtkSourceView adds support for syntax highlighting, undo/redo, file loading and saving, search and replace, a completion system, printing, displaying line numbers, and other features typical of a source code editor.
homepage: https://wiki.gnome.org/Projects/GtkSourceView
version toolchain 3.24.11 GCCcore/10.2.0 3.24.11 GCCcore/8.2.0 4.4.0 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Gubbins/","title":"Gubbins","text":"Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.
homepage: https://sanger-pathogens.github.io/gubbins
version toolchain 2.4.0 system 3.3.5 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Guile/","title":"Guile","text":"Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.
homepage: http://www.gnu.org/software/guile
version toolchain 1.8.8 GCCcore/5.4.0 1.8.8 GCCcore/6.4.0 1.8.8 GCCcore/7.3.0 1.8.8 GCCcore/8.2.0 1.8.8 GCCcore/8.3.0 1.8.8 GCCcore/9.3.0 1.8.8 GNU/4.9.3-2.25 1.8.8 foss/2016a 1.8.8 foss/2016b 1.8.8 foss/2017a 1.8.8 intel/2016a 1.8.8 intel/2016b 2.0.11 GCC/4.9.3-2.25 2.0.11 foss/2016a 2.0.14 GCCcore/13.3.0 2.2.2 GCCcore/6.4.0 2.2.4 GCCcore/7.3.0 2.2.4 GCCcore/9.3.0 2.2.7 GCCcore/10.3.0 3.0.10 GCCcore/13.3.0 3.0.7 GCCcore/11.2.0 3.0.8 GCCcore/11.3.0 3.0.9 GCCcore/10.2.0 3.0.9 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Gurobi/","title":"Gurobi","text":"The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms.
homepage: https://www.gurobi.com
version versionsuffix toolchain 10.0.1 GCCcore/11.3.0 10.0.1 GCCcore/12.2.0 11.0.0 GCCcore/12.3.0 11.0.2 GCCcore/12.3.0 6.5.1 system 6.5.2 system 7.0.1 system 7.5.2 -Python-3.6.4 intel/2018a 7.5.2 system 8.1.1 system 9.0.0 -Python-3.7.4 GCCcore/8.3.0 9.0.0 -Python-3.6.6 foss/2018b 9.0.0 -Python-3.6.6 intel/2018b 9.0.0 system 9.0.1 -Python-3.8.2 GCCcore/9.3.0 9.0.1 system 9.0.3 GCCcore/10.2.0 9.0.3 system 9.1.0 system 9.1.1 GCCcore/10.2.0 9.1.2 GCCcore/10.2.0 9.1.2 GCCcore/10.3.0 9.1.2 system 9.5.0 GCCcore/10.3.0 9.5.0 GCCcore/11.2.0 9.5.2 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/Gymnasium/","title":"Gymnasium","text":"Gymnasium is an open source Python library for developing and comparing reinforcement learning algorithms by providing a standard API to communicate between learning algorithms and environments, as well as a standard set of environments compliant with that API.
homepage: https://gymnasium.farama.org/
version toolchain 0.29.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/g2clib/","title":"g2clib","text":"Library contains GRIB2 encoder/decoder ('C' version).
homepage: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/
version toolchain 1.6.0 GCCcore/8.3.0 1.6.0 GCCcore/9.3.0 1.6.0 foss/2018b 1.6.0 intel/2017a 1.6.0 intel/2017b 1.6.0 intel/2018a 1.6.0 intel/2018b 1.6.3 GCCcore/10.2.0 1.6.3 GCCcore/10.3.0 1.6.3 GCCcore/11.2.0 1.7.0 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/g2lib/","title":"g2lib","text":"Library contains GRIB2 encoder/decoder and search/indexing routines.
homepage: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/
version toolchain 1.4.0 intel/2017a 1.4.0 intel/2017b 1.4.0 intel/2018a 3.1.0 GCCcore/8.3.0 3.1.0 GCCcore/9.3.0 3.1.0 foss/2018b 3.1.0 intel/2018b 3.2.0 GCCcore/10.2.0 3.2.0 GCCcore/10.3.0 3.2.0 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/g2log/","title":"g2log","text":"g2log, efficient asynchronous logger using C++11
homepage: https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11
version toolchain 1.0 GCCcore/8.3.0 1.0 foss/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gRPC/","title":"gRPC","text":"gRPC is a modern, open source, high-performance remote procedure call (RPC) framework that can run anywhere. gRPC enables client and server applications to communicate transparently, and simplifies the building of connected systems.
homepage: https://grpc.io/
version toolchain 1.44.0 GCCcore/11.2.0 1.57.0 GCCcore/12.3.0 1.62.1 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gSOAP/","title":"gSOAP","text":"The gSOAP toolkit is a C and C++ software development toolkit for SOAP and REST XML Web services and generic C/C++ XML data bindings. The toolkit analyzes WSDLs and XML schemas (separately or as a combined set) and maps the XML schema types and the SOAP/REST XML messaging protocols to easy-to-use and efficient C and C++ code. It also supports exposing (legacy) C and C++ applications as XML Web services by auto-generating XML serialization code and WSDL specifications. Or you can simply use it to automatically convert XML to/from C and C++ data. The toolkit supports options to generate pure ANSI C or C++ with or without STL.
homepage: https://www.cs.fsu.edu/~engelen/soap.html
version toolchain 2.8.100 GCCcore/8.3.0 2.8.48 GCCcore/6.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gap/","title":"gap","text":"GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory.
homepage: https://www.gap-system.org
version toolchain 4.11.0 foss/2019a 4.12.2 foss/2022a 4.13.0 foss/2023b 4.9.3 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gappa/","title":"gappa","text":"gappa is a collection of commands for working with phylogenetic data. Its main focus are evolutionary placements of short environmental sequences on a reference phylogenetic tree. Such data is typically produced by tools like EPA-ng, RAxML-EPA or pplacer and usually stored in jplace files.
homepage: https://github.com/lczech/gappa
version toolchain 0.7.1 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/garnett/","title":"garnett","text":"Garnett is a software package that faciliates automated cell type classification from single-cell expression data.
homepage: https://cole-trapnell-lab.github.io/garnett
version versionsuffix toolchain 0.1.20 -R-4.0.3 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gawk/","title":"gawk","text":"The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code.
homepage: https://www.gnu.org/software/gawk
version toolchain 5.1.0 GCC/10.2.0 5.1.1 GCC/10.3.0 5.1.1 GCC/11.2.0 5.1.1 GCC/11.3.0 5.3.0 GCC/12.2.0 5.3.0 GCC/12.3.0 5.3.0 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gbasis/","title":"gbasis","text":"Python library for analytical evaluation and integration of Gaussian-type basis functions and related quantities.
homepage: https://github.com/theochem/gbasis
version toolchain 20210904 intel/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gbs2ploidy/","title":"gbs2ploidy","text":"Inference of Ploidy from (Genotyping-by-Sequencing) GBS Data
homepage: https://cran.r-project.org/web/packages/gbs2ploidy
version versionsuffix toolchain 1.0 -R-3.4.3 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gc/","title":"gc","text":"The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.
homepage: https://hboehm.info/gc/
version toolchain 7.4.4 GCC/4.9.3-2.25 7.4.4 foss/2016a 7.6.0 GCCcore/6.4.0 7.6.10 GCCcore/8.2.0 7.6.12 GCCcore/8.3.0 7.6.12 GCCcore/9.3.0 7.6.4 GCCcore/7.3.0 8.0.4 GCCcore/10.3.0 8.2.0 GCCcore/11.2.0 8.2.2 GCCcore/10.2.0 8.2.2 GCCcore/11.3.0 8.2.4 GCCcore/12.3.0 8.2.6 GCCcore/13.2.0 8.2.6 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gcccuda/","title":"gcccuda","text":"GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.
homepage: <(none)>
version toolchain 2016.08 system 2017b system 2018a system 2018b system 2019a system 2019b system 2020a system 2020b system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gcloud/","title":"gcloud","text":"Libraries and tools for interacting with Google Cloud products and services.
homepage: https://cloud.google.com/sdk
version toolchain 382.0.0 system 472.0.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gcsfs/","title":"gcsfs","text":"Pythonic file-system interface for Google Cloud Storage.
homepage: https://github.com/fsspec/gcsfs
version toolchain 2023.12.2.post1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gdbgui/","title":"gdbgui","text":"Browser-based frontend to gdb (gnu debugger). Add breakpoints, view the stack, visualize data structures, and more in C, C++, Go, Rust, and Fortran. Run gdbgui from the terminal and a new tab will open in your browser.
homepage: https://gdbgui.com
version versionsuffix toolchain 0.13.1.2 -Python-3.7.2 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gdbm/","title":"gdbm","text":"GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing and work similar to the standard UNIX dbm. These routines are provided to a programmer needing to create and manipulate a hashed database.
homepage: https://www.gnu.org.ua/software/gdbm/
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homepage: https://pypi.python.org/pypi/gdist
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","boost":0.5},{"location":"version-specific/supported-software/g/gearshifft/","title":"gearshifft","text":"Benchmark Suite for Heterogenuous FFT Implementations
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version toolchain 0.4.0 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://github.com/biocore/gemelli
version toolchain 0.0.9 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://genozip.com
version toolchain 13.0.5 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://pypi.python.org/pypi/gensim
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homepage: https://github.com/ULB-Metronu/georges
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","boost":0.5},{"location":"version-specific/supported-software/g/geosphere/","title":"geosphere","text":"Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.
homepage: https://cran.r-project.org/web/packages/geosphere/index.html
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","boost":0.5},{"location":"version-specific/supported-software/g/gettext/","title":"gettext","text":"GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation
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","boost":0.5},{"location":"version-specific/supported-software/g/gfbf/","title":"gfbf","text":"GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.
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","boost":0.5},{"location":"version-specific/supported-software/g/gffread/","title":"gffread","text":"GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.
homepage: https://github.com/gpertea/gffread
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homepage: https://github.com/daler/gffutils
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","boost":0.5},{"location":"version-specific/supported-software/g/giac/","title":"giac","text":"Giac is a C++ library, it is the CAS computing kernel. It may be used inside other C++ programs, and also Python, Java and Javascript programs.
homepage: https://www-fourier.ujf-grenoble.fr/~parisse/giac.html
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homepage: http://libungif.sourceforge.net/
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homepage: https://github.com/kohler/gifsicle
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version toolchain 2017b system 2018a system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/giolfc/","title":"giolfc","text":"GCC based compiler toolchain with CUDA support, and including IntelMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
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version toolchain 2017b system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 2016a system 2017.10 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 20240306 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 2018b system 2020b system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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","boost":0.5},{"location":"version-specific/supported-software/g/gompi/","title":"gompi","text":"GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
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","boost":0.5},{"location":"version-specific/supported-software/g/gompic/","title":"gompic","text":"GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.
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version toolchain 20220610 intel/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://cloud.google.com/storage/docs/gsutil
version toolchain 5.10 GCCcore/11.2.0 5.29 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gsw/","title":"gsw","text":"This Python implementation of the Thermodynamic Equation of Seawater 2010 (TEOS-10) is based primarily on numpy ufunc wrappers of the GSW-C implementation. This library replaces the original python-gsw pure-python implementation.. The primary reasons for this change are that by building on the C implementation we reduce code duplication and we gain an immediate update to the 75-term equation. Additional benefits include a major increase in speed, a reduction in memory usage, and the inclusion of more functions. The penalty is that a C (or MSVC C++ for Windows) compiler is required to build the package from source.
homepage: https://github.com/TEOS-10/GSW-python
version toolchain 3.6.16 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gtk-doc/","title":"gtk-doc","text":"Documentation tool for public library API
homepage: https://gitlab.gnome.org/GNOME/gtk-doc
version toolchain 1.34.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/guenomu/","title":"guenomu","text":"guenomu is a software written in C that estimates the species tree for a given set of gene families.
homepage: https://bitbucket.org/leomrtns/guenomu
version versionsuffix toolchain 2019.07.05 -mpi iimpi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/g/gzip/","title":"gzip","text":"gzip (GNU zip) is a popular data compression program as a replacement for compress
homepage: https://www.gnu.org/software/gzip/
version toolchain 1.10 GCCcore/10.2.0 1.10 GCCcore/10.3.0 1.10 GCCcore/11.2.0 1.10 GCCcore/8.2.0 1.10 GCCcore/8.3.0 1.10 GCCcore/9.3.0 1.12 GCCcore/11.3.0 1.12 GCCcore/12.2.0 1.12 GCCcore/12.3.0 1.13 GCCcore/13.2.0 1.13 GCCcore/13.3.0 1.8 GCCcore/5.4.0 1.8 GCCcore/6.3.0 1.8 GCCcore/6.4.0 1.9 GCCcore/7.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/","title":"List of supported software (h)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- h4toh5
- H5hut
- h5netcdf
- h5py
- Hadoop
- HAL
- hampel
- hanythingondemand
- HAPGEN2
- HarfBuzz
- Harminv
- harmony
- hatch-jupyter-builder
- hatchling
- HBase
- HD-BET
- HDBSCAN
- HDDM
- HDF
- HDF-EOS
- HDF-EOS2
- HDF-EOS5
- HDF5
- hdf5storage
- HDFView
- hdWGCNA
- HEALPix
- Health-GPS
- heaptrack
- hector
- HeFFTe
- Hello
- help2man
- HepMC
- HepMC3
- HERRO
- hevea
- HF-Datasets
- HH-suite
- HiC-Pro
- hic-straw
- HiCExplorer
- HiCMatrix
- hierfstat
- hifiasm
- HighFive
- HiGHS
- Highway
- HIP
- hipify-clang
- HIPS
- hipSYCL
- hiredis
- HISAT2
- histolab
- hivtrace
- hl7apy
- HLAminer
- hmmcopy_utils
- HMMER
- HMMER2
- hmmlearn
- HOME
- HOMER
- HOOMD-blue
- Horovod
- horton
- how_are_we_stranded_here
- HPCC
- HPCG
- HPCX
- HPDBSCAN
- HPL
- htop
- HTSeq
- HTSlib
- HTSplotter
- hub
- humann
- hunspell
- hwloc
- Hybpiper
- Hydra
- Hyperopt
- HyperQueue
- hyperspy
- HyPhy
- HyPo
- hypothesis
- Hypre
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/H5hut/","title":"H5hut","text":"HDF5 Utility Toolkit: High-Performance I/O Library for Particle-based Simulations
homepage: https://amas.psi.ch/H5hut/
version toolchain 1.99.13 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HAL/","title":"HAL","text":"HAL is a structure to efficiently store and index multiple genome alignments and ancestral reconstructions. HAL is a graph-based representation which provides several advantages over matrix/block-based formats such as MAF, such as improved scalability and the ability to perform queries with respect to an arbitrary reference or subtree. This package includes the HAL API and several analysis and conversion tools which are described below. HAL files are presently stored in either HDF5 or mmap format, but we note that the tools and most of the API are format-independent, so other databases could be implemented in the future.
homepage: https://github.com/ComparativeGenomicsToolkit/hal
version toolchain 2.1 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HAPGEN2/","title":"HAPGEN2","text":"'HAPGEN2' simulates case control datasets at SNP markers.
homepage: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html
version toolchain 2.2.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HBase/","title":"HBase","text":"Apache HBase. is the Hadoop database, a distributed, scalable, big data store.
homepage: http://hbase.apache.org/
version toolchain 1.0.2 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HD-BET/","title":"HD-BET","text":"Tool for brain extraction.
homepage: https://github.com/MIC-DKFZ/HD-BET
version versionsuffix toolchain 20220318 -CUDA-11.3.1 foss/2021a 20220318 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HDBSCAN/","title":"HDBSCAN","text":"The hdbscan library is a suite of tools to use unsupervised learning to find clusters, or dense regions, of a dataset. The primary algorithm is HDBSCAN* as proposed by Campello, Moulavi, and Sander. The library provides a high performance implementation of this algorithm, along with tools for analysing the resulting clustering.
homepage: http://hdbscan.readthedocs.io/en/latest/
version versionsuffix toolchain 0.8.24 -Python-3.7.4 foss/2019b 0.8.27 foss/2021a 0.8.29 foss/2022a 0.8.38.post1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HDDM/","title":"HDDM","text":"HDDM is a Puthon toolbox for hierarchical Bayesian parameter estimation of the Drift Diffusion Model (via PyMC).
homepage: http://ski.clps.brown.edu/hddm_docs
version versionsuffix toolchain 0.6.1 -Python-3.6.6 intel/2018b 0.7.5 -Python-2.7.16 intel/2019b 0.7.5 -Python-3.7.4 intel/2019b 0.9.9 foss/2021b 0.9.9 intel/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HDF-EOS/","title":"HDF-EOS","text":"HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath.
homepage: https://hdfeos.org/
version toolchain 2.20 GCCcore/10.2.0 2.20 GCCcore/7.3.0 2.20 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HDF-EOS2/","title":"HDF-EOS2","text":"HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath.
homepage: https://hdfeos.org/
version toolchain 3.0 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HDF-EOS5/","title":"HDF-EOS5","text":"HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath.
homepage: https://hdfeos.org/
version toolchain 1.16 foss/2018b 1.16 gompi/2019b 1.16 gompi/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HDF/","title":"HDF","text":"HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.
homepage: http://support.hdfgroup.org/products/hdf4/
version versionsuffix toolchain 4.2.11 intel/2016a 4.2.12 intel/2017a 4.2.13 GCCcore/6.4.0 4.2.13 -no-netcdf intel/2017a 4.2.14 GCCcore/6.4.0 4.2.14 GCCcore/7.3.0 4.2.14 GCCcore/8.2.0 4.2.14 GCCcore/8.3.0 4.2.15 GCCcore/10.2.0 4.2.15 GCCcore/10.3.0 4.2.15 GCCcore/11.2.0 4.2.15 GCCcore/11.3.0 4.2.15 GCCcore/12.2.0 4.2.15 GCCcore/9.3.0 4.2.16-2 GCCcore/12.3.0 4.2.16-2 GCCcore/13.2.0 4.2.16 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HDF5/","title":"HDF5","text":"HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
homepage: https://support.hdfgroup.org/HDF5/
version versionsuffix toolchain 1.10.0-patch1 foss/2016b 1.10.0-patch1 intel/2016b 1.10.0-patch1 intel/2017.01 1.10.0-patch1 intel/2017a 1.10.1 foss/2017a 1.10.1 foss/2017b 1.10.1 foss/2018a 1.10.1 fosscuda/2017b 1.10.1 intel/2017a 1.10.1 intel/2017b 1.10.1 intel/2018.00 1.10.1 intel/2018.01 1.10.1 intel/2018a 1.10.1 intelcuda/2017b 1.10.1 iomkl/2017b 1.10.1 iomkl/2018a 1.10.2 PGI/18.4-GCC-6.4.0-2.28 1.10.2 foss/2018b 1.10.2 fosscuda/2018b 1.10.2 intel/2018b 1.10.2 iomkl/2018b 1.10.5 -serial GCC/8.3.0 1.10.5 gompi/2019a 1.10.5 gompi/2019b 1.10.5 gompic/2019a 1.10.5 gompic/2019b 1.10.5 iimpi/2019a 1.10.5 iimpi/2019b 1.10.5 iimpic/2019a 1.10.5 iimpic/2019b 1.10.5 iompi/2019b 1.10.6 gompi/2020a 1.10.6 gompic/2020a 1.10.6 iimpi/2020a 1.10.6 iimpic/2020a 1.10.6 iompi/2020a 1.10.7 gompi/2020b 1.10.7 gompi/2021a 1.10.7 gompic/2020b 1.10.7 iimpi/2020b 1.10.7 iimpi/2021a 1.10.7 iimpic/2020b 1.10.7 iompi/2021a 1.10.8 gompi/2021b 1.10.8 gompi/2022a 1.12.0 gompi/2020a 1.12.0 iimpi/2020a 1.12.1 gompi/2021a 1.12.1 gompi/2021b 1.12.1 iimpi/2021b 1.12.2 -serial GCC/11.3.0 1.12.2 -serial NVHPC/22.7-CUDA-11.7.0 1.12.2 gompi/2022a 1.12.2 iimpi/2022a 1.12.2 nvompi/2022.07 1.13.1 -serial GCC/11.3.0 1.13.1 gompi/2022a 1.13.1 iimpi/2022a 1.14.0 gompi/2022b 1.14.0 gompi/2023a 1.14.0 iimpi/2022b 1.14.0 iimpi/2023a 1.14.3 gompi/2023b 1.14.3 iimpi/2023b 1.8.10 -serial GCC/4.8.1 1.8.11 -serial GCC/4.8.1 1.8.12 foss/2018b 1.8.12 intel/2016b 1.8.13 foss/2018b 1.8.16 -serial foss/2016a 1.8.16 foss/2016a 1.8.16 -serial gimkl/2.11.5 1.8.16 intel/2016.02-GCC-4.9 1.8.16 -serial intel/2016a 1.8.16 intel/2016a 1.8.16 iomkl/2016.07 1.8.16 iomkl/2016.09-GCC-4.9.3-2.25 1.8.17 -serial GCC/5.4.0-2.26 1.8.17 -serial foss/2016a 1.8.17 foss/2016a 1.8.17 foss/2016b 1.8.17 intel/2016a 1.8.17 -serial intel/2016b 1.8.17 intel/2016b 1.8.18 foss/2016b 1.8.18 foss/2017a 1.8.18 gimkl/2017a 1.8.18 intel/2016b 1.8.18 intel/2017.01 1.8.18 -serial intel/2017a 1.8.18 intel/2017a 1.8.19 foss/2017a 1.8.19 foss/2017b 1.8.19 intel/2017a 1.8.19 intel/2017b 1.8.20 foss/2018a 1.8.20 gmpolf/2017.10 1.8.20 intel/2017b 1.8.20 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HDFView/","title":"HDFView","text":"HDFView is a visual tool for browsing and editing HDF4 and HDF5 files.
homepage: https://support.hdfgroup.org/products/java/hdfview/
version versionsuffix toolchain 2.14 -Java-1.8.0_152-centos6 system 2.14 -Java-1.8.0_152-centos7 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HEALPix/","title":"HEALPix","text":"Hierarchical Equal Area isoLatitude Pixelation of a sphere.
homepage: http://healpix.sourceforge.net/
version toolchain 3.50 GCCcore/7.3.0 3.50 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HERRO/","title":"HERRO","text":"HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).
homepage: https://github.com/lbcb-sci/herro
version toolchain 0.1.0_20240808 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HF-Datasets/","title":"HF-Datasets","text":"The largest hub of ready-to-use datasets for ML models with fast, easy-to-use and efficient data manipulation tools.
homepage: https://github.com/huggingface/datasets
version toolchain 2.18.0 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HH-suite/","title":"HH-suite","text":"The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
homepage: https://github.com/soedinglab/hh-suite
version versionsuffix toolchain 3.0-beta.3 intel/2018a 3.2.0 foss/2019b 3.2.0 fosscuda/2019b 3.3.0 foss/2020a 3.3.0 gompi/2020b 3.3.0 gompi/2021a 3.3.0 gompi/2021b 3.3.0 gompi/2022a 3.3.0 gompi/2023a 3.3.0 -Python-3.7.4 gompic/2019b 3.3.0 gompic/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HIP/","title":"HIP","text":"HIP is a C++ Runtime API and Kernel Language that allows developers to create portable applications for AMD and NVIDIA GPUs from single source code.
homepage: https://github.com/ROCm-Developer-Tools/HIP
version versionsuffix toolchain 4.5.0 -amd GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HIPS/","title":"HIPS","text":"HIPS (Hierarchical Iterative Parallel Solver) is a scientific library that provides an efficient parallel iterative solver for very large sparse linear systems.
homepage: http://hips.gforge.inria.fr/
version toolchain 1.2b-rc5 foss/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HISAT2/","title":"HISAT2","text":"HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).
homepage: https://ccb.jhu.edu/software/hisat2/index.shtml
version toolchain 2.0.3-beta intel/2016a 2.0.4 foss/2016b 2.0.5 intel/2017a 2.1.0 foss/2017b 2.1.0 foss/2018b 2.1.0 intel/2017a 2.1.0 intel/2017b 2.1.0 intel/2018a 2.2.0 foss/2018b 2.2.1 foss/2019b 2.2.1 foss/2020a 2.2.1 gompi/2020b 2.2.1 gompi/2021a 2.2.1 gompi/2021b 2.2.1 gompi/2022a 2.2.1 gompi/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HLAminer/","title":"HLAminer","text":"HLAminer is a software for HLA predictions from next-generation shotgun (NGS) sequence read data and supports direct read alignment and targeted de novo assembly of sequence reads.
homepage: http://www.bcgsc.ca/platform/bioinfo/software/hlaminer
version versionsuffix toolchain 1.4 -Perl-5.28.0 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HMMER/","title":"HMMER","text":"HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
homepage: http://hmmer.org/
version toolchain 3.1b2 GCC/6.4.0-2.28 3.1b2 foss/2016a 3.1b2 foss/2016b 3.1b2 foss/2018a 3.1b2 iccifort/2017.4.196-GCC-6.4.0-2.28 3.1b2 intel/2017a 3.1b2 intel/2018a 3.2.1 GCC/8.2.0-2.31.1 3.2.1 foss/2018b 3.2.1 gompi/2019b 3.2.1 iccifort/2019.1.144-GCC-8.2.0-2.31.1 3.2.1 iimpi/2019b 3.2.1 intel/2018b 3.3.1 gompi/2020a 3.3.1 iimpi/2020a 3.3.2 gompi/2019b 3.3.2 gompi/2020a 3.3.2 gompi/2020b 3.3.2 gompi/2021a 3.3.2 gompi/2021b 3.3.2 gompi/2022a 3.3.2 gompi/2022b 3.3.2 gompic/2020b 3.3.2 iimpi/2020b 3.3.2 iimpi/2021b 3.4 gompi/2023a 3.4 gompi/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HMMER2/","title":"HMMER2","text":"HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments.
homepage: http://hmmer.org
version toolchain 2.3.2 GCC/10.2.0 2.3.2 GCC/10.3.0 2.3.2 GCC/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HOME/","title":"HOME","text":"HOME (histogram of methylation) is a python package for differential methylation region (DMR) identification. The method uses histogram of methylation features and the linear Support Vector Machine (SVM) to identify DMRs from whole genome bisulfite sequencing (WGBS) data.
homepage: https://github.com/ListerLab/HOME
version versionsuffix toolchain 0.9 -Python-2.7.13 foss/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HOMER/","title":"HOMER","text":"HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line programs for unix-style operating systems written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.
homepage: http://homer.ucsd.edu/homer/
version versionsuffix toolchain 4.11 -R-4.3.2 foss/2023a 4.11.1 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HOOMD-blue/","title":"HOOMD-blue","text":"HOOMD-blue is a general-purpose particle simulation toolkit, implementing molecular dynamics and hard particle Monte Carlo optimized for fast execution on both GPUs and CPUs.
homepage: https://glotzerlab.engin.umich.edu/hoomd-blue/
version versionsuffix toolchain 4.0.1 -CUDA-11.7.0 foss/2022a 4.0.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HPCC/","title":"HPCC","text":"HPC Challenge is a benchmark suite that measures a range memory access patterns. The HPC Challenge benchmark consists of basically 7 tests: HPL, DGEMM, STREAM, PTRANS, RandomAccess, FFT, Communication bandwidth and latency
homepage: https://hpcchallenge.org/
version toolchain 1.5.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HPCG/","title":"HPCG","text":"The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.
homepage: https://software.sandia.gov/hpcg
version toolchain 3.0 foss/2016b 3.0 foss/2018b 3.0 intel/2018b 3.1 foss/2018b 3.1 foss/2021a 3.1 foss/2021b 3.1 foss/2022a 3.1 foss/2022b 3.1 foss/2023a 3.1 intel/2018b 3.1 intel/2021a 3.1 intel/2021b 3.1 intel/2022a 3.1 intel/2022b 3.1 intel/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HPCX/","title":"HPCX","text":"The Mellanox HPC-X Toolkit is a comprehensive MPI and SHMEM/PGAS software suite for high performance computing environments
homepage: http://www.mellanox.com/page/products_dyn?product_family=189&mtag=hpc-x
version toolchain 2.3.0 GCC/8.2.0-2.31.1 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HPDBSCAN/","title":"HPDBSCAN","text":"Highly parallel density based spatial clustering for application with noise
homepage: https://github.com/Markus-Goetz/hpdbscan
version toolchain 20171110 foss/2017b 20210826 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HPL/","title":"HPL","text":"HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.
homepage: https://www.netlib.org/benchmark/hpl/
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","boost":0.5},{"location":"version-specific/supported-software/h/HTSeq/","title":"HTSeq","text":"A framework to process and analyze data from high-throughput sequencing (HTS) assays
homepage: https://www-huber.embl.de/users/anders/HTSeq/
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","boost":0.5},{"location":"version-specific/supported-software/h/HTSlib/","title":"HTSlib","text":"A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
homepage: https://www.htslib.org/
version versionsuffix toolchain 1.10.2 GCC/8.3.0 1.10.2 GCC/9.3.0 1.10.2 iccifort/2019.5.281 1.11 GCC/10.2.0 1.11 iccifort/2020.4.304 1.12 GCC/10.2.0 1.12 GCC/10.3.0 1.12 GCC/9.3.0 1.14 GCC/11.2.0 1.15.1 GCC/11.3.0 1.17 GCC/12.2.0 1.18 GCC/12.3.0 1.19.1 GCC/13.2.0 1.2.1 foss/2016b 1.3 foss/2016a 1.3 intel/2016a 1.3.1 foss/2016a 1.3.1 foss/2016b 1.3.1 intel/2016b 1.3.2 intel/2016b 1.4 foss/2016b 1.4 intel/2016b 1.4.1 foss/2016a 1.4.1 intel/2017a 1.6 foss/2016b 1.6 foss/2017b 1.6 intel/2017b 1.7 intel/2018a 1.8 GCC/6.4.0-2.28 1.8 foss/2018a 1.8 intel/2018a 1.9 GCC/6.4.0-2.28 1.9 GCC/8.2.0-2.31.1 1.9 foss/2018b 1.9 iccifort/2017.4.196-GCC-6.4.0-2.28 1.9 iccifort/2019.1.144-GCC-8.2.0-2.31.1 1.9 intel/2018b 20160107 -PacBio intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HTSplotter/","title":"HTSplotter","text":"HTSplotter allows an end-to-end data processing and analysis of chemical and genetic in vitro perturbation screens.
homepage: https://github.com/CBIGR/HTSplotter
version toolchain 0.15 foss/2022a 2.11 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/Hadoop/","title":"Hadoop","text":"Hadoop MapReduce by Cloudera
homepage: https://archive.cloudera.com/cdh5/cdh/5/
version versionsuffix toolchain 2.10.0 -native-Java-1.8 GCCcore/10.2.0 2.10.0 -native GCCcore/8.3.0 2.4.0 -seagate-722af1-native system 2.5.0-cdh5.3.1 -native system 2.6.0-cdh5.12.0 -native system 2.6.0-cdh5.4.5 -native system 2.6.0-cdh5.7.0 -native system 2.6.0-cdh5.8.0 -native system 2.9.2 -native GCCcore/7.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HarfBuzz/","title":"HarfBuzz","text":"HarfBuzz is an OpenType text shaping engine.
homepage: https://www.freedesktop.org/wiki/Software/HarfBuzz
version toolchain 1.1.3 foss/2016a 1.1.3 intel/2016a 1.2.7 foss/2016a 1.2.7 intel/2016a 1.3.1 foss/2016b 1.3.1 intel/2016b 1.3.1 intel/2017a 1.5.1 intel/2017a 1.7.1 foss/2017b 1.7.1 intel/2017b 1.7.5 foss/2018a 1.7.5 intel/2018a 1.9.0 fosscuda/2018b 2.2.0 foss/2018b 2.2.0 fosscuda/2018b 2.4.0 GCCcore/8.2.0 2.6.4 GCCcore/8.3.0 2.6.4 GCCcore/9.3.0 2.6.7 GCCcore/10.2.0 2.8.1 GCCcore/10.3.0 2.8.2 GCCcore/11.2.0 4.2.1 GCCcore/11.3.0 5.3.1 GCCcore/12.2.0 5.3.1 GCCcore/12.3.0 8.2.2 GCCcore/13.2.0 9.0.0 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/Harminv/","title":"Harminv","text":"Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.
homepage: http://ab-initio.mit.edu/wiki/index.php/Harminv
version toolchain 1.4 foss/2016a 1.4.1 foss/2017b 1.4.1 foss/2018a 1.4.1 intel/2018a 1.4.1 intel/2020a 1.4.2 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HeFFTe/","title":"HeFFTe","text":"Highly Efficient FFT for Exascale (HeFFTe) library
homepage: https://icl.utk.edu/fft
version toolchain 1.0 foss/2020a 2.4.0 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/Health-GPS/","title":"Health-GPS","text":"Health-GPS microsimulation is part of the STOP project, and support researchers and policy makers in the analysis of the health and economic impacts of alternative measures to tackle chronic diseases and obesity in children. The model reproduces the characteristics of a population and simulates key individual event histories associated with key components of relevant behaviours, such as physical activity, and diseases such as diabetes or cancer. To run the test-jobs with HealthGPS.Tests the data-directory, found in your installation folder, must be in the current path.
homepage: https://github.com/imperialCHEPI/healthgps
version toolchain 1.1.3.0 GCCcore/11.3.0 1.2.2.0 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/Hello/","title":"Hello","text":"The GNU Hello program produces a familiar, friendly greeting. Yes, this is another implementation of the classic program that prints \"Hello, world!\" when you run it. However, unlike the minimal version often seen, GNU Hello processes its argument list to modify its behavior, supports greetings in many languages, and so on.
homepage: https://www.gnu.org/software/hello/
version toolchain 2.10 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HepMC/","title":"HepMC","text":"HepMC is a standard for storing Monte Carlo event data.
homepage: http://hepmc.web.cern.ch/hepmc/
version toolchain 2.06.11 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HepMC3/","title":"HepMC3","text":"HepMC is a standard for storing Monte Carlo event data.
homepage: http://hepmc.web.cern.ch/hepmc/
version toolchain 3.2.5 GCC/11.3.0 3.2.6 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HiC-Pro/","title":"HiC-Pro","text":"HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps.
homepage: http://nservant.github.io/HiC-Pro
version versionsuffix toolchain 2.9.0 -Python-2.7.12 foss/2016b 3.1.0 -R-4.2.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HiCExplorer/","title":"HiCExplorer","text":"HiCexplorer addresses the common tasks of Hi-C analysis from processing to visualization.
homepage: http://hicexplorer.readthedocs.org/
version versionsuffix toolchain 2.1.1 -Python-3.6.4 foss/2018a 3.7.2 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HiCMatrix/","title":"HiCMatrix","text":"This library implements the central class of HiCExplorer to manage Hi-C interaction matrices.
homepage: https://github.com/deeptools/HiCMatrix
version toolchain 17 foss/2022a 17.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HiGHS/","title":"HiGHS","text":"Open source serial and parallel solvers for large-scale sparse linear programming (LP), mixed-integer programming (MIP), and quadratic programming (QP) models.
homepage: https://ergo-code.github.io/HiGHS
version toolchain 1.7.0 gfbf/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HighFive/","title":"HighFive","text":"HighFive is a modern header-only C++11 friendly interface for libhdf5.
homepage: https://github.com/BlueBrain/HighFive
version toolchain 2.6.2 gompi/2021a 2.6.2 gompi/2022a 2.7.1 gompi/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/Highway/","title":"Highway","text":"Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same operation to 'lanes'.
homepage: https://github.com/google/highway
version toolchain 0.12.2 GCCcore/10.2.0 0.12.2 GCCcore/10.3.0 1.0.3 GCCcore/11.3.0 1.0.3 GCCcore/12.2.0 1.0.4 GCCcore/11.3.0 1.0.4 GCCcore/12.3.0 1.0.7 GCCcore/13.2.0 1.2.0 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/Horovod/","title":"Horovod","text":"Horovod is a distributed training framework for TensorFlow.
homepage: https://github.com/uber/horovod
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","boost":0.5},{"location":"version-specific/supported-software/h/HyPhy/","title":"HyPhy","text":"HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning
homepage: https://veg.github.io/hyphy-site/
version toolchain 2.3.13 foss/2016b 2.5.1 gompi/2019a 2.5.33 gompi/2021a 2.5.60 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HyPo/","title":"HyPo","text":"HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies
homepage: https://github.com/kensung-lab/hypo
version versionsuffix toolchain 1.0.3 -Python-3.7.4 GCC/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/Hybpiper/","title":"Hybpiper","text":"HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts/modules that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.
homepage: https://github.com/mossmatters/HybPiper
version toolchain 2.1.6 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/Hydra/","title":"Hydra","text":"Hydra is an open-source Python framework that simplifies the development of research and other complex applications. The key feature is the ability to dynamically create a hierarchical configuration by composition and override it through config files and the command line. The name Hydra comes from its ability to run multiple similar jobs - much like a Hydra with multiple heads.
homepage: https://hydra.cc/
version toolchain 1.1.1 GCCcore/10.3.0 1.3.2 GCCcore/11.3.0 1.3.2 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/HyperQueue/","title":"HyperQueue","text":"HyperQueue lets you build a computation plan consisting of a large amount of tasks and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs and distributes them to fully utilize allocated nodes. You thus do not have to manually aggregate your tasks into SLURM/PBS jobs.
homepage: https://it4innovations.github.io/hyperqueue/
version toolchain 0.13.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/Hyperopt/","title":"Hyperopt","text":"hyperopt is a Python library for optimizing over awkward search spaces with real-valued, discrete, and conditional dimensions.
homepage: https://hyperopt.github.io/hyperopt/
version versionsuffix toolchain 0.1 -Python-2.7.14 intel/2017b 0.1.1 -Python-3.6.6 intel/2018b 0.2.4 -Python-3.7.4-Java-1.8 intel/2019b 0.2.5 fosscuda/2020b 0.2.7 foss/2021a 0.2.7 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/Hypre/","title":"Hypre","text":"Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.
homepage: https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html
version toolchain 2.11.1 foss/2016a 2.11.1 intel/2016a 2.14.0 foss/2018a 2.14.0 intel/2018a 2.15.1 foss/2019a 2.15.1 intel/2019a 2.18.2 foss/2019b 2.18.2 foss/2020a 2.18.2 intel/2019b 2.18.2 intel/2020a 2.20.0 foss/2020b 2.20.0 intel/2020b 2.21.0 foss/2021a 2.21.0 fosscuda/2020b 2.21.0 intel/2021a 2.24.0 intel/2021b 2.25.0 foss/2022a 2.27.0 foss/2022b 2.29.0 foss/2023a 2.31.0 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/h4toh5/","title":"h4toh5","text":"The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.
homepage: http://www.hdfgroup.org/h4toh5/
version versionsuffix toolchain 2.2.2 -linux-x86_64-static system 2.2.3 foss/2018b 2.2.3 gompi/2019b 2.2.3 gompi/2020b 2.2.5 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/h5netcdf/","title":"h5netcdf","text":"A Python interface for the netCDF4 file-format that reads and writes local or remote HDF5 files directly via h5py or h5pyd, without relying on the Unidata netCDF library.
homepage: https://h5netcdf.org/
version toolchain 1.1.0 foss/2021b 1.2.0 foss/2022a 1.2.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/h5py/","title":"h5py","text":"HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.
homepage: https://www.h5py.org/
version versionsuffix toolchain 2.10.0 -Python-3.7.4 foss/2019b 2.10.0 -serial-Python-3.7.4 foss/2019b 2.10.0 -Python-3.8.2 foss/2020a 2.10.0 -Python-3.7.4 fosscuda/2019b 2.10.0 -Python-3.8.2 fosscuda/2020a 2.10.0 -Python-3.7.4 intel/2019b 2.10.0 -Python-2.7.18 intel/2020a 2.10.0 -Python-3.8.2 intel/2020a 2.10.0 -Python-3.7.4 intelcuda/2019b 2.10.0 -Python-3.8.2 intelcuda/2020a 2.5.0 -Python-2.7.11-HDF5-1.8.16-serial foss/2016a 2.5.0 -Python-2.7.11-HDF5-1.8.16 foss/2016a 2.5.0 -Python-3.5.1-HDF5-1.8.16 foss/2016a 2.5.0 -Python-2.7.11-HDF5-1.8.16-serial intel/2016a 2.5.0 -Python-2.7.11-HDF5-1.8.16 intel/2016a 2.6.0 -Python-2.7.12-HDF5-1.10.0-patch1 foss/2016b 2.6.0 -Python-2.7.12-HDF5-1.8.17 foss/2016b 2.6.0 -Python-2.7.12-HDF5-1.8.18 foss/2016b 2.6.0 -Python-3.5.2-HDF5-1.10.0-patch1 foss/2016b 2.6.0 -Python-3.5.2-HDF5-1.8.18 foss/2016b 2.6.0 -Python-2.7.11 intel/2016a 2.6.0 -Python-2.7.12-HDF5-1.10.0-patch1 intel/2016b 2.6.0 -Python-2.7.12-HDF5-1.8.17 intel/2016b 2.6.0 -Python-2.7.12-HDF5-1.8.18 intel/2016b 2.6.0 -Python-3.5.2-HDF5-1.10.0-patch1 intel/2016b 2.6.0 -Python-3.5.2-HDF5-1.8.17 intel/2016b 2.6.0 -Python-3.5.2-HDF5-1.8.18 intel/2016b 2.7.0 -Python-2.7.13-HDF5-1.10.1 foss/2017a 2.7.0 -Python-2.7.13-HDF5-1.8.19 foss/2017a 2.7.0 -Python-3.6.1-HDF5-1.10.1 foss/2017a 2.7.0 -Python-3.6.1-HDF5-1.8.19 foss/2017a 2.7.0 -Python-2.7.12 intel/2016b 2.7.0 -Python-2.7.13 intel/2017a 2.7.0 -Python-3.6.1-HDF5-1.10.0-patch1 intel/2017a 2.7.0 -Python-3.6.1 intel/2017a 2.7.1 -Python-2.7.14 foss/2017b 2.7.1 -Python-3.6.3 foss/2017b 2.7.1 -Python-2.7.14 foss/2018a 2.7.1 -Python-3.6.4 foss/2018a 2.7.1 -Python-2.7.14 fosscuda/2017b 2.7.1 -Python-3.6.3 fosscuda/2017b 2.7.1 -Python-2.7.13 intel/2017a 2.7.1 -Python-3.6.1 intel/2017a 2.7.1 -Python-2.7.14 intel/2017b 2.7.1 -Python-3.6.3 intel/2017b 2.7.1 -Python-2.7.14-serial intel/2018a 2.7.1 -Python-2.7.14 intel/2018a 2.7.1 -Python-3.6.4 intel/2018a 2.8.0 -Python-2.7.15 foss/2018b 2.8.0 -Python-3.6.6 foss/2018b 2.8.0 -Python-2.7.15 fosscuda/2018b 2.8.0 -Python-3.6.6 fosscuda/2018b 2.8.0 -Python-2.7.15-serial intel/2018b 2.8.0 -Python-2.7.15 intel/2018b 2.8.0 -Python-3.6.6 intel/2018b 2.9.0 foss/2019a 2.9.0 fosscuda/2019a 2.9.0 intel/2019a 2.9.0 intelcuda/2019a 3.1.0 foss/2020b 3.1.0 fosscuda/2020b 3.1.0 intel/2020b 3.1.0 intelcuda/2020b 3.11.0 foss/2023b 3.2.1 foss/2021a 3.2.1 gomkl/2021a 3.6.0 foss/2021b 3.6.0 intel/2021b 3.7.0 foss/2022a 3.7.0 intel/2022a 3.8.0 foss/2022b 3.9.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hampel/","title":"hampel","text":"The Hampel filter is generally used to detect anomalies in data with a timeseries structure. It basically consists of a sliding window of a parameterizable size. For each window, each observation will be compared with the Median Absolute Deviation (MAD). The observation will be considered an outlier in the case in which it exceeds the MAD by n times (the parameter n is also parameterizable).
homepage: https://github.com/MichaelisTrofficus/hampel_filter
version toolchain 0.0.5 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hanythingondemand/","title":"hanythingondemand","text":"HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.
homepage: https://github.com/hpcugent/hanythingondemand
version versionsuffix toolchain 3.0.0 -cli system 3.0.1 -cli system 3.0.2 -cli system 3.0.3 -cli system 3.0.4 -cli system 3.1.0 -cli system 3.1.0 -Python-2.7.11 intel/2016a 3.1.1 -cli system 3.1.1 -Python-2.7.11 intel/2016a 3.1.2 -cli system 3.1.2 -Python-2.7.11 intel/2016a 3.1.3 -cli system 3.1.3 -Python-2.7.12 intel/2016b 3.1.4 -cli system 3.1.4 -Python-2.7.12 intel/2016b 3.2.0 -cli system 3.2.0 -Python-2.7.12 intel/2016b 3.2.2 -cli system 3.2.2 -Python-2.7.12 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/harmony/","title":"harmony","text":"Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets.
homepage: https://portals.broadinstitute.org/harmony
version versionsuffix toolchain 0.1.0-20210528 -R-4.0.3 foss/2020b 1.0.0-20200224 -R-4.0.0 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hatch-jupyter-builder/","title":"hatch-jupyter-builder","text":"Hatch Jupyter Builder is a plugin for the hatchling Python build backend. It is primarily targeted for package authors who are providing JavaScript as part of their Python packages. Typical use cases are Jupyter Lab Extensions and Jupyter Widgets.
homepage: https://hatch-jupyter-builder.readthedocs.io
version toolchain 0.9.1 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hatchling/","title":"hatchling","text":"Extensible, standards compliant build backend used by Hatch, a modern, extensible Python project manager.
homepage: https://hatch.pypa.io
version toolchain 1.18.0 GCCcore/12.3.0 1.18.0 GCCcore/13.2.0 1.24.2 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hdWGCNA/","title":"hdWGCNA","text":"hdWGCNA is an R package for performing weighted gene co-expression network analysis (WGCNA) in high dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics. hdWGCNA is highly modular and can construct context-specific co-expression networks across cellular and spatial hierarchies. hdWGNCA identifies modules of highly co-expressed genes and provides context for these modules via statistical testing and biological knowledge sources. hdWGCNA uses datasets formatted as Seurat objects.
homepage: https://smorabit.github.io/hdWGCNA/
version versionsuffix toolchain 0.3.00 -R-4.3.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hdf5storage/","title":"hdf5storage","text":"This Python package provides high level utilities to read/write a variety of Python types to/from HDF5 (Heirarchal Data Format) formatted files. This package also provides support for MATLAB MAT v7.3 formatted files, which are just HDF5 files with a different extension and some extra meta-data. All of this is done without pickling data. Pickling is bad for security because it allows arbitrary code to be executed in the interpreter. One wants to be able to read possibly HDF5 and MAT files from untrusted sources, so pickling is avoided in this package.
homepage: https://pythonhosted.org/hdf5storage/
version toolchain 0.1.15 foss/2019a 0.1.15 fosscuda/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/heaptrack/","title":"heaptrack","text":"A heap memory profiler for Linux.
homepage: http://milianw.de/blog/heaptrack-a-heap-memory-profiler-for-linux
version toolchain 1.1.0 foss/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hector/","title":"hector","text":"This is the repository for Hector, an open source, object-oriented, simple global climate carbon-cycle model. It runs essentially instantaneously while still representing the most critical global scale earth system processes, and is one of a class of models heavily used for for emulating complex climate models and uncertainty analyses.
homepage: https://github.com/JGCRI/hector
version toolchain 2.5.0 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/help2man/","title":"help2man","text":"help2man produces simple manual pages from the '--help' and '--version' output of other commands.
homepage: https://www.gnu.org/software/help2man/
version toolchain 1.47.10 GCCcore/9.1.0 1.47.10 GCCcore/9.2.0 1.47.12 GCCcore/9.3.0 1.47.15 GCCcore/10.1.0 1.47.16 GCCcore/10.2.0 1.47.4 GCCcore/5.4.0 1.47.4 GCCcore/6.3.0 1.47.4 GCCcore/6.4.0 1.47.4 GCCcore/7.1.0 1.47.4 GCCcore/7.2.0 1.47.4 GCCcore/7.3.0 1.47.4 GCCcore/system 1.47.4 gimkl/2017a 1.47.4 intel/2016b 1.47.4 system 1.47.5 GCCcore/5.5.0 1.47.6 GCCcore/8.1.0 1.47.7 GCCcore/8.2.0 1.47.8 GCCcore/7.4.0 1.47.8 GCCcore/8.3.0 1.47.8 GCCcore/8.4.0 1.48.3 GCCcore/10.3.0 1.48.3 GCCcore/11.1.0 1.48.3 GCCcore/11.2.0 1.48.3 GCCcore/9.4.0 1.49.2 GCCcore/11.3.0 1.49.2 GCCcore/12.1.0 1.49.2 GCCcore/12.2.0 1.49.2 GCCcore/9.5.0 1.49.3 GCCcore/11.4.0 1.49.3 GCCcore/12.3.0 1.49.3 GCCcore/13.1.0 1.49.3 GCCcore/13.2.0 1.49.3 GCCcore/13.3.0 1.49.3 GCCcore/14.1.0 1.49.3 GCCcore/14.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hevea/","title":"hevea","text":"A quite complete and fast LATEX to HTML translator
homepage: http://pauillac.inria.fr/~maranget/hevea/
version toolchain 2.36 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hic-straw/","title":"hic-straw","text":"Straw is a library which allows rapid streaming of contact data from .hic files.
homepage: https://github.com/aidenlab/straw
version toolchain 1.3.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hierfstat/","title":"hierfstat","text":"Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy.
homepage: https://cran.r-project.org/package=hierfstat
version versionsuffix toolchain 0.5-7 -R-4.0.0-Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hifiasm/","title":"hifiasm","text":"Hifiasm: a haplotype-resolved assembler for accurate Hifi reads.
homepage: https://github.com/chhylp123/hifiasm
version toolchain 0.15.2 GCCcore/10.3.0 0.15.2 GCCcore/9.3.0 0.16.1 GCCcore/10.3.0 0.19.5 GCCcore/11.2.0 0.19.7 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hipSYCL/","title":"hipSYCL","text":"hipSYCL is a modern SYCL implementation targeting CPUs and GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP
homepage: https://github.com/illuhad/hipSYCL
version toolchain 0.9.1 GCC/10.2.0 0.9.1 gcccuda/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hipify-clang/","title":"hipify-clang","text":"Hipify-clang is a clang-based tool for translating CUDA sources into HIP sources. It translates CUDA source into an abstract syntax tree, which is traversed by transformation matchers. After applying all the matchers, the output HIP source is produced.
homepage: https://github.com/ROCm-Developer-Tools/HIPIFY
version toolchain 4.2.0 gcccuda/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hiredis/","title":"hiredis","text":"Hiredis is a minimalistic C client library for the Redis database. It is minimalistic because it just adds minimal support for the protocol, but at the same time it uses a high level printf-alike API in order to make it much higher level than otherwise suggested by its minimal code base and the lack of explicit bindings for every Redis command.
homepage: https://github.com/redis/hiredis
version toolchain 1.0.2 GCCcore/11.2.0 1.0.2 GCCcore/11.3.0 1.2.0 GCCcore/12.2.0 1.2.0 GCCcore/12.3.0 1.2.0 GCCcore/13.2.0 1.2.0 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/histolab/","title":"histolab","text":"Library for Digital Pathology Image Processing
homepage: https://github.com/histolab/histolab
version toolchain 0.4.1 foss/2021a 0.4.1 foss/2021b 0.6.0 foss/2022a 0.7.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hivtrace/","title":"hivtrace","text":"HIV-TRACE is an application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.
homepage: https://github.com/veg/hivtrace
version toolchain 0.6.2 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hl7apy/","title":"hl7apy","text":"Python library to parse, create and handle HL7 v2 messages.
homepage: https://github.com/crs4/hl7apy
version versionsuffix toolchain 1.3.3 -Python-3.7.4 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hmmcopy_utils/","title":"hmmcopy_utils","text":"Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.
homepage: https://github.com/shahcompbio/hmmcopy_utils
version toolchain 20210728 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hmmlearn/","title":"hmmlearn","text":"hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models
homepage: https://github.com/hmmlearn/hmmlearn
version versionsuffix toolchain 0.2.0 -Python-2.7.14 intel/2017b 0.2.0 -Python-3.6.4 intel/2018a 0.3.0 foss/2022b 0.3.0 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/horton/","title":"horton","text":"HORTON is a Helpful Open-source Research TOol for N-fermion systems, written primarily in the Python programming language. (HORTON is named after the helpful pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON is to provide a platform for testing new ideas on the quantum many-body problem at a reasonable computational cost. Although HORTON is primarily designed to be a quantum-chemistry program, it can perform computations involving model Hamiltonians, and could be extended for computations in nuclear physics.
homepage: https://theochem.github.io/horton
version versionsuffix toolchain 2.1.1 -Python-2.7.15 foss/2018b 2.1.1 -Python-2.7.15 intel/2018b 2.1.1 -Python-2.7.18 intel/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/how_are_we_stranded_here/","title":"how_are_we_stranded_here","text":"Python package for testing strandedness of RNA-Seq fastq files
homepage: https://github.com/signalbash/how_are_we_stranded_here
version toolchain 1.0.1 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/htop/","title":"htop","text":"An interactive process viewer for Unix
homepage: http://hisham.hm/htop/
version toolchain 2.0.0 system 2.0.1 system 3.2.1 system 3.2.2 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hub/","title":"hub","text":"hub is a command-line wrapper for git that makes you better at GitHub.
homepage: https://hub.github.com/
version versionsuffix toolchain 2.2.2 -linux-amd64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/humann/","title":"humann","text":"HUMAnN v3 is a pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data. Sequencing a metagenome typically produces millions of short DNA/RNA reads. This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question: What are the microbes in my community-of-interest doing (or capable of doing)?
homepage: http://huttenhower.sph.harvard.edu/humann
version toolchain 3.6 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hunspell/","title":"hunspell","text":"Hunspell is a spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding.
homepage: http://hunspell.github.io/
version toolchain 1.6.1 intel/2017a 1.7.0 GCCcore/8.2.0 1.7.1 GCCcore/11.2.0 1.7.1 GCCcore/11.3.0 1.7.2 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hwloc/","title":"hwloc","text":"The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.
homepage: https://www.open-mpi.org/projects/hwloc/
version toolchain 1.10.0 GCC/4.9.2 1.10.1 GCC/4.8.4 1.10.1 GNU/4.9.2-2.25 1.11.0 GNU/4.9.3-2.25 1.11.1 GCC/4.9.3 1.11.10 GCCcore/7.3.0 1.11.11 GCCcore/8.2.0 1.11.12 GCCcore/8.3.0 1.11.2 GCC/4.9.3-2.25 1.11.2 GNU/4.9.3-2.25 1.11.3 GCC/5.2.0 1.11.3 GCC/5.3.0-2.26 1.11.3 GCC/5.4.0-2.26 1.11.3 GCC/6.1.0-2.27 1.11.3 PGI/16.3-GCC-4.9.3-2.25 1.11.3 PGI/16.4-GCC-5.3.0-2.26 1.11.3 iccifort/2016.3.210-GCC-4.9.3-2.25 1.11.3 iccifort/2016.3.210-GCC-5.4.0-2.26 1.11.3 intel/2016a 1.11.3 intel/2016b 1.11.4 GCC/6.2.0-2.27 1.11.4 PGI/16.7-GCC-5.4.0-2.26 1.11.4 iccifort/2017.1.132-GCC-5.4.0-2.26 1.11.5 GCC/5.4.0-2.26 1.11.5 GCC/6.3.0-2.27 1.11.5 iccifort/2017.1.132-GCC-6.3.0-2.27 1.11.6 GCC/6.3.0-2.28 1.11.7 GCCcore/5.4.0 1.11.7 GCCcore/6.4.0 1.11.8 GCCcore/6.4.0 1.11.8 GCCcore/7.2.0 1.11.8 intel/2017a 1.7.2 GCC/4.8.2 1.8.1 GCC/4.8.2 1.8.1 GCC/4.8.3 1.9 GCC/4.8.3 2.0.2 GCCcore/8.2.0 2.0.3 GCCcore/8.3.0 2.1.0 GCCcore/9.2.0 2.10.0 GCCcore/13.3.0 2.2.0 GCCcore/10.2.0 2.2.0 GCCcore/9.3.0 2.4.1 GCCcore/10.3.0 2.5.0 GCCcore/11.2.0 2.7.1 GCCcore/11.3.0 2.8.0 GCCcore/12.2.0 2.9.1 GCCcore/12.3.0 2.9.2 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hyperspy/","title":"hyperspy","text":"HyperSpy is an open source Python library which provides tools to facilitate the interactive data analysis of multi-dimensional datasets that can be described as multi-dimensional arrays of a given signal (e.g. a 2D array of spectra a.k.a spectrum image)
homepage: https://hyperspy.org/
version versionsuffix toolchain 1.1.1 -Python-3.5.2 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/h/hypothesis/","title":"hypothesis","text":"Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work.
homepage: https://github.com/HypothesisWorks/hypothesis
version versionsuffix toolchain 4.23.4 GCCcore/8.2.0 4.39.3 -Python-3.6.4 intel/2018a 4.44.2 -Python-3.7.4 GCCcore/8.3.0 4.5.0 -Python-3.6.6 foss/2018b 4.5.0 -Python-3.6.6 fosscuda/2018b 4.53.1 GCCcore/10.2.0 4.57.1 -Python-2.7.18 GCCcore/11.2.0 5.41.2 GCCcore/10.2.0 5.41.5 GCCcore/10.2.0 5.6.0 -Python-3.8.2 GCCcore/9.3.0 6.103.1 GCCcore/13.3.0 6.13.1 GCCcore/10.3.0 6.14.6 GCCcore/11.2.0 6.46.7 GCCcore/11.3.0 6.68.2 GCCcore/12.2.0 6.7.0 GCCcore/10.2.0 6.82.0 GCCcore/12.3.0 6.90.0 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/","title":"List of supported software (i)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- i-cisTarget
- i-PI
- I-TASSER
- i7z
- ICA-AROMA
- icc
- iccifort
- iccifortcuda
- iced
- ichorCNA
- icmake
- ICON
- iCount
- ICU
- IDBA-UD
- idemux
- IDG
- ieeg-cli
- IEntropy
- ifort
- IgBLAST
- IGMPlot
- igraph
- IGV
- igv-reports
- igvShiny
- IGVTools
- iibff
- iimkl
- iimpi
- iimpic
- IJulia
- ILAMB
- ilastik-napari
- IMa2
- IMa2p
- IMAGE
- imagecodecs
- imageio
- ImageJ
- ImageMagick
- imake
- Imath
- IMB
- imbalanced-learn
- imgaug
- imkl
- imkl-FFTW
- IML
- Imlib2
- immunedeconv
- IMOD
- impi
- IMPUTE2
- imutils
- InChI
- indicators
- Inelastica
- inferCNV
- infercnvpy
- Inferelator
- Infernal
- inflection
- Infomap
- inih
- inline
- InParanoid
- inputproto
- Inspector
- IntaRNA
- INTEGRATE
- INTEGRATE-Neo
- intel
- intel-compilers
- IntelClusterChecker
- intelcuda
- IntelDAAL
- IntelPython
- InterOp
- InterProScan
- InterProScan_data
- intervaltree
- intervaltree-python
- intltool
- io_lib
- ioapi
- iodata
- iomkl
- iompi
- IonQuant
- IOR
- IOzone
- iperf
- IPM
- Ipopt
- ipp
- IPy
- ipympl
- ipyparallel
- ipyrad
- IPython
- IQ-TREE
- Iris
- IRkernel
- irodsfs
- IronPython
- ISA-L
- ISL
- isoCirc
- IsoformSwitchAnalyzeR
- IsoNet
- IsoQuant
- IsoSeq
- ispc
- itac
- ITK
- itpp
- ITSTool
- ITSx
- iVar
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/I-TASSER/","title":"I-TASSER","text":"I-TASSER is a set of pre-compiled binaries and scripts for protein structure and function modelling and comparison.
homepage: http://zhanglab.ccmb.med.umich.edu/I-TASSER/
version toolchain 4.0 system 4.2 system 5.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/ICA-AROMA/","title":"ICA-AROMA","text":"ICA-AROMA (i.e. 'ICA-based Automatic Removal Of Motion Artifacts') concerns a data-driven method to identify and remove motion-related independent components from fMRI data.
homepage: https://github.com/maartenmennes/ICA-AROMA
version versionsuffix toolchain 0.4.4-beta -Python-3.6.6 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/ICON/","title":"ICON","text":"ICON is a flexible, scalable, high-performance modelling framework for weather, climate and environmental prediction that provides actionable information for society and advances our understanding of the Earth's climate system.
homepage: https://www.icon-model.org/
version toolchain 2024.01 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/ICU/","title":"ICU","text":"ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
homepage: http://site.icu-project.org/home
version toolchain 61.1 GCCcore/6.4.0 61.1 GCCcore/7.3.0 64.2 GCCcore/8.2.0 64.2 GCCcore/8.3.0 65.1 GCCcore/8.3.0 66.1 GCCcore/9.3.0 67.1 GCCcore/10.2.0 69.1 GCCcore/10.3.0 69.1 GCCcore/11.2.0 71.1 GCCcore/11.3.0 72.1 GCCcore/12.2.0 73.2 GCCcore/12.3.0 74.1 GCCcore/13.2.0 75.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IDBA-UD/","title":"IDBA-UD","text":"IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.
homepage: https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/
version toolchain 1.1.3 GCC/10.2.0 1.1.3 GCC/10.3.0 1.1.3 GCC/11.2.0 1.1.3 GCC/8.2.0-2.31.1 1.1.3 GCC/8.3.0 1.1.3 GCC/9.3.0 1.1.3 foss/2018a 1.1.3 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IDG/","title":"IDG","text":"Image Domain Gridding (IDG) is a fast method for convolutional resampling (gridding/degridding) of radio astronomical data (visibilities). Direction dependent effects (DDEs) or A-tems can be applied in the gridding process. The algorithm is described in \"Image Domain Gridding: a fast method for convolutional resampling of visibilities\", Van der Tol (2018). The implementation is described in \"Radio-astronomical imaging on graphics processors\", Veenboer (2020). Please cite these papers in publications using IDG.
homepage: https://idg.readthedocs.io/
version toolchain 1.2.0 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IEntropy/","title":"IEntropy","text":"Here, by deriving entropy decomposition formula, we proposed a feature selection method, intrinsic entropy (IE) model, to identify the informative genes for accurately clustering analysis.
homepage: https://github.com/LinLi-0909/IEntropy
version versionsuffix toolchain 2024.06.12 -R-4.3.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IGMPlot/","title":"IGMPlot","text":"IGMPlot is a free open-source program developed to identify molecular interactions and prepare data to build 2D and 3D representations of them in the molecular environment.
homepage: http://igmplot.univ-reims.fr
version toolchain 2.4.2 GCC/8.3.0 2.4.2 iccifort/2019.5.281 2.6.9b GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IGV/","title":"IGV","text":"This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files.
homepage: https://www.broadinstitute.org/software/igv/
version versionsuffix toolchain 2.12.3 -Java-11 system 2.16.0 -Java-11 system 2.17.4 -Java-17 system 2.3.68 -Java-1.7.0_80 system 2.3.80 -Java-1.7.0_80 system 2.5.0 -Java-11 system 2.8.0 -Java-11 system 2.9.4 -Java-11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IGVTools/","title":"IGVTools","text":"This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline.
homepage: http://www.broadinstitute.org/software/igv/
version versionsuffix toolchain 2.3.68 -Java-1.7.0_80 system 2.3.72 -Java-1.7.0_80 system 2.3.75 -Java-1.7.0_80 system 2.4.18 -Java-1.8 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IJulia/","title":"IJulia","text":"Julia kernel for Jupyter
homepage: https://github.com/JuliaLang/IJulia.jl
version versionsuffix toolchain 1.23.3 -Julia-1.6.7 system 1.24.0 -Julia-1.8.5 system 1.24.2 -Julia-1.10.3 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/ILAMB/","title":"ILAMB","text":"The International Land Model Benchmarking (ILAMB) project is a model-data intercomparison and integration project designed to improve the performance of land models and, in parallel, improve the design of new measurement campaigns to reduce uncertainties associated with key land surface processes.
homepage: https://www.ilamb.org/
version versionsuffix toolchain 2.5 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IMAGE/","title":"IMAGE","text":"IMAGE (Motif Activity and Gene Expression changes of transcription factors) is software for integrated analysis of motif activity and gene expression changes of transcription factors. IMAGE makes prediction of causal transcription factors based on transcriptome profiling and genome-wide maps of enhancer activity.
homepage: https://github.com/JesperGrud/IMAGE
version toolchain 1.1 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IMB/","title":"IMB","text":"The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes
homepage: https://software.intel.com/en-us/articles/intel-mpi-benchmarks
version toolchain 2018.1 intel/2017a 2019.3 gompi/2019a 2019.3 iimpi/2019a 2021.3 gompi/2020b 2021.3 gompi/2021b 2021.3 gompi/2022a 2021.3 gompi/2022b 2021.3 iimpi/2022a 2021.3 iimpi/2022b 4.1 foss/2016a 4.1 foss/2017a 4.1 intel/2017.02 4.1 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IML/","title":"IML","text":"IML is a free library of C source code which implements algorithms for computing exact solutions to dense systems of linear equations over the integers.
homepage: https://cs.uwaterloo.ca/~astorjoh/iml.html
version toolchain 1.0.5 gfbf/2022a 1.0.5 gfbf/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IMOD/","title":"IMOD","text":"IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, and John Heumann at the University of Colorado.
homepage: https://bio3d.colorado.edu/imod/
version versionsuffix toolchain 4.11.5 foss/2020b 4.11.5 fosscuda/2020b 4.7.15 _RHEL6-64_CUDA6.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IMPUTE2/","title":"IMPUTE2","text":"IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009
homepage: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html
version versionsuffix toolchain 2.3.0 _x86_64_dynamic system 2.3.0 _x86_64_static system 2.3.2 _x86_64_dynamic system 2.3.2 _x86_64_static system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IMa2/","title":"IMa2","text":"IMa2 is a progam for population genetic analysis that can handle two or more populations.
homepage: https://bio.cst.temple.edu/~hey/software/software.htm#IMa2
version toolchain 8.27.12 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IMa2p/","title":"IMa2p","text":"IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC based method for inferring population demography under the IM (Isolation with Migration) model. http://dx.doi.org/10.1111/1755-0998.12437
homepage: https://github.com/arunsethuraman/ima2p
version toolchain 20151123 foss/2016a 20160804 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/INTEGRATE-Neo/","title":"INTEGRATE-Neo","text":"INTEGRATE-Neo is a gene fusion neoantigen discovering tool using next-generation sequencing data. It is written in C++ and Python.
homepage: <>
version versionsuffix toolchain 1.2.1 -Python-3.6.6 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/INTEGRATE/","title":"INTEGRATE","text":"INTEGRATE is a tool calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data. It is highly sensitive and accurate by applying a fast split-read mapping algorithm based on Burrow-Wheeler transform.
homepage: https://sourceforge.net/p/integrate-fusion/wiki/Home/
version toolchain 0.2.6 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IOR/","title":"IOR","text":"The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces.
homepage: https://github.com/chaos/ior
version versionsuffix toolchain 3.0.1 -mpiio foss/2016a 3.2.1 gompi/2019b 3.3.0 gompi/2020b 3.3.0 gompi/2021a 3.3.0 gompi/2022a 4.0.0 gompi/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IOzone/","title":"IOzone","text":"IOzone is a filesystem benchmark tool. The benchmark generates and measures a variety of file operations. Iozone has been ported to many machines and runs under many operating systems.
homepage: http://www.iozone.org/
version toolchain 3.434 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IPM/","title":"IPM","text":"IPM is a portable profiling infrastructure for parallel codes. It provides a low-overhead profile of application performance and resource utilization in a parallel program. Communication, computation, and IO are the primary focus.
homepage: https://github.com/nerscadmin/IPM
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","boost":0.5},{"location":"version-specific/supported-software/i/IPy/","title":"IPy","text":"Class and tools for handling of IPv4 and IPv6 addresses and networks
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version toolchain 0.83 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IPython/","title":"IPython","text":"IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing.
homepage: https://ipython.org/index.html
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","boost":0.5},{"location":"version-specific/supported-software/i/IQ-TREE/","title":"IQ-TREE","text":"Efficient phylogenomic software by maximum likelihood
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","boost":0.5},{"location":"version-specific/supported-software/i/IRkernel/","title":"IRkernel","text":"The R kernel for the 'Jupyter' environment executes R code which the front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network.
homepage: https://irkernel.github.io
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","boost":0.5},{"location":"version-specific/supported-software/i/ISA-L/","title":"ISA-L","text":"Intelligent Storage Acceleration Library
homepage: https://github.com/intel/isa-l
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","boost":0.5},{"location":"version-specific/supported-software/i/ISL/","title":"ISL","text":"isl is a library for manipulating sets and relations of integer points bounded by linear constraints.
homepage: http://isl.gforge.inria.fr/
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","boost":0.5},{"location":"version-specific/supported-software/i/ITK/","title":"ITK","text":"Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data.
homepage: https://itk.org
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","boost":0.5},{"location":"version-specific/supported-software/i/ITSTool/","title":"ITSTool","text":"ITS Tool allows you to translate your XML documents with PO files, using rules from the W3C Internationalization Tag Set (ITS) to determine what to translate and how to separate it into PO file messages.
homepage: https://itstool.org/
version versionsuffix toolchain 2.0.5 -Python-2.7.15 foss/2018b 2.0.5 -Python-2.7.14 intel/2018a 2.0.6 -Python-3.7.2 GCCcore/8.2.0 2.0.7 GCCcore/11.3.0 2.0.7 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/ITSx/","title":"ITSx","text":"ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing.
homepage: https://microbiology.se/software/itsx/
version toolchain 1.1.2 GCCcore/9.3.0 1.1.3 GCCcore/10.3.0 1.1.3 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IgBLAST/","title":"IgBLAST","text":"IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.
homepage: https://ncbi.github.io/igblast
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","boost":0.5},{"location":"version-specific/supported-software/i/ImageJ/","title":"ImageJ","text":"Image Processing and Analysis in Java
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version versionsuffix toolchain 1.51a system 1.51i system 1.51k system 1.52q -Java-1.8 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/ImageMagick/","title":"ImageMagick","text":"ImageMagick is a software suite to create, edit, compose, or convert bitmap images
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version versionsuffix toolchain 6.9.4-8 intel/2016a 7.0.1-6 intel/2016a 7.0.1-9 intel/2016a 7.0.10-1 GCCcore/9.3.0 7.0.10-35 GCCcore/10.2.0 7.0.11-14 GCCcore/10.3.0 7.0.2-9 intel/2016a 7.0.3-1 intel/2016b 7.0.5-10 foss/2016b 7.0.5-4 intel/2017a 7.0.7-14 foss/2017b 7.0.7-14 intel/2017b 7.0.7-15 GCCcore/6.4.0 7.0.7-26 foss/2018a 7.0.7-30 -Ghostscript-9.22-cairo-1.14.12 GCCcore/6.4.0 7.0.7-30 GCCcore/6.4.0 7.0.7-39 -Ghostscript-9.23-cairo-1.14.12 GCCcore/6.4.0 7.0.7-8 -JasPer-1.900.1 intel/2017a 7.0.8-11 GCCcore/7.3.0 7.0.8-46 GCCcore/8.2.0 7.0.9-5 GCCcore/8.3.0 7.1.0-37 GCCcore/11.3.0 7.1.0-4 GCCcore/11.2.0 7.1.0-53 GCCcore/12.2.0 7.1.1-15 GCCcore/12.3.0 7.1.1-34 GCCcore/13.2.0 7.1.1-38 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/Imath/","title":"Imath","text":"Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics
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","boost":0.5},{"location":"version-specific/supported-software/i/Imlib2/","title":"Imlib2","text":"This is the Imlib 2 library - a library that does image file loading and saving as well as rendering, manipulation, arbitrary polygon support, etc. It does ALL of these operations FAST. Imlib2 also tries to be highly intelligent about doing them, so writing naive programs can be done easily, without sacrificing speed.
homepage: https://docs.enlightenment.org/api/imlib2/html/
version toolchain 1.5.1 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/InChI/","title":"InChI","text":"The IUPAC International Chemical Identifier (InChI TM) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations.
homepage: https://www.inchi-trust.org/
version toolchain 1.06 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/InParanoid/","title":"InParanoid","text":"InParanoid: ortholog groups with inparalogs.
homepage: https://inparanoid.sbc.su.se
version toolchain 5.0-20220607 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/Inelastica/","title":"Inelastica","text":"Python package for eigenchannels, vibrations and inelastic electron transport based on SIESTA/TranSIESTA DFT.
homepage: https://github.com/tfrederiksen/inelastica
version versionsuffix toolchain 1.3.5 -Python-2.7.15 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/Inferelator/","title":"Inferelator","text":"Inferelator 3.0 is a package for gene regulatory network inference that is based on regularized regression.
homepage: https://github.com/flatironinstitute/inferelator
version toolchain 0.6.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/Infernal/","title":"Infernal","text":"Infernal (\"INFERence of RNA ALignment\") is for searching DNA sequence databases for RNA structure and sequence similarities.
homepage: http://eddylab.org/infernal/
version toolchain 1.1.2 foss/2016b 1.1.2 foss/2018b 1.1.2 intel/2017a 1.1.2 intel/2018b 1.1.4 foss/2020b 1.1.4 foss/2021a 1.1.4 foss/2021b 1.1.4 foss/2022a 1.1.4 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/Infomap/","title":"Infomap","text":"Multi-level network clustering based on the Map equation.
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version toolchain 20190308 GCC/8.2.0-2.31.1 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/Inspector/","title":"Inspector","text":"Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications
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","boost":0.5},{"location":"version-specific/supported-software/i/IntaRNA/","title":"IntaRNA","text":"Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites
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version versionsuffix toolchain 2.3.1 -Python-2.7.15 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IntelClusterChecker/","title":"IntelClusterChecker","text":"Verifies cluster components work together \u2015 for - better uptime and productivity and lower total - cost of ownership (TCO)
homepage: https://software.intel.com/en-us/intel-cluster-checker
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","boost":0.5},{"location":"version-specific/supported-software/i/IntelDAAL/","title":"IntelDAAL","text":"Intel\u00ae Data Analytics Acceleration Library (Intel\u00ae DAAL) is the library of Intel\u00ae architecture optimized building blocks covering all stages of data analytics: data acquisition from a data source, preprocessing, transformation, data mining, modeling, validation, and decision making.
homepage: https://software.intel.com/en-us/daal
version toolchain 2019.4.007 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IntelPython/","title":"IntelPython","text":"Intel\u00ae Distribution for Python. Powered by Anaconda. Accelerating Python* performance on modern architectures from Intel.
homepage: https://software.intel.com/en-us/intel-distribution-for-python
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","boost":0.5},{"location":"version-specific/supported-software/i/InterOp/","title":"InterOp","text":"The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files produced by Illumina sequencers including NextSeq 1k/2k and NovaSeqX. These libraries are backwards compatible and capable of supporting prior releases of the software, with one exception: GA systems have been excluded.
homepage: https://illumina.github.io/interop/
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","boost":0.5},{"location":"version-specific/supported-software/i/InterProScan/","title":"InterProScan","text":"InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource.
homepage: http://www.ebi.ac.uk/interpro/
version toolchain 5.26-65.0 intel/2017b 5.27-66.0 intel/2017b 5.28-67.0 intel/2018a 5.52-86.0 GCCcore/10.3.0 5.55-88.0 foss/2021a 5.62-94.0 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/InterProScan_data/","title":"InterProScan_data","text":"InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource [data only].
homepage: https://www.ebi.ac.uk/interpro/
version toolchain 5.55-88.0 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IonQuant/","title":"IonQuant","text":"IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies. IonQuant is available as part of FragPipe.
homepage: https://ionquant.nesvilab.org/
version versionsuffix toolchain 1.10.12 -Java-11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/Ipopt/","title":"Ipopt","text":"Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization.
homepage: https://coin-or.github.io/Ipopt
version toolchain 3.12.13 intel/2019a 3.12.9 foss/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/Iris/","title":"Iris","text":"A module for improving the insertion sequences of structural variant calls
homepage: https://github.com/mkirsche/Iris
version versionsuffix toolchain 1.0.5 -Java-15 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IronPython/","title":"IronPython","text":"IronPython is an open-source implementation of the Python programming language which is tightly integrated with the .NET Framework. IronPython can use the .NET Framework and Python libraries, and other .NET languages can use Python code just as easily.
homepage: http://ironpython.net/
version toolchain 2.7 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IsoNet/","title":"IsoNet","text":"IsoNet stands for for ISOtropic reconstructioN of Electron Tomography. It trains deep convolutional neural networks to reconstruct meaningful contents in the mis sing wedge for electron tomography, and to increase signal-to-noise ratio, using the information learned from the original tomogram. The software requires tomograms as input. Observing at about 30A resolution, the IsoNet generated tomograms are largely isotropic.
homepage: https://github.com/Heng-Z/IsoNet
version toolchain 0.1_20210822_04_674f67f fosscuda/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IsoQuant/","title":"IsoQuant","text":"IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores. IsoQuant allows to reconstruct and quantify transcript models with high precision and decent recall. If the reference annotation is given, IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. IsoQuant further performs annotated gene, isoform, exon and intron quantification. If reads are grouped (e.g. according to cell type), counts are reported according to the provided grouping.
homepage: https://github.com/ablab/IsoQuant
version toolchain 3.3.0 foss/2022b 3.5.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IsoSeq/","title":"IsoSeq","text":"IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique, allows to process the ever-increasing yield of PacBio machines with similar performance to IsoSeq versions 1 and 2. Starting with version 3.4, support for UMI and cell barcode based deduplication has been added.
homepage: https://github.com/PacificBiosciences/ioseq3
version versionsuffix toolchain 3.8.2 -linux-x86_64 system 4.0.0 -linux-x86_64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/IsoformSwitchAnalyzeR/","title":"IsoformSwitchAnalyzeR","text":"Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.
homepage: https://bioconductor.org/packages/release/bioc/html/IsoformSwitchAnalyzeR.html
version versionsuffix toolchain 1.18.0 -R-4.2.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/i-PI/","title":"i-PI","text":"A Python wrapper for (ab initio) (path integrals) molecular dynamics
homepage: https://github.com/i-pi/i-pi
version versionsuffix toolchain 1.0-20160213 -Python-2.7.11 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/i-cisTarget/","title":"i-cisTarget","text":"An integrative genomics method for the prediction of regulatory features and cis-regulatory modules in Human, Mouse, and Fly
homepage: https://gbiomed.kuleuven.be/apps/lcb/i-cisTarget
version versionsuffix toolchain 20160602 -Python-2.7.11 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/i7z/","title":"i7z","text":"A better i7 (and now i3, i5) reporting tool for Linux
homepage: https://github.com/ajaiantilal/i7z
version toolchain 20131012 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/iCount/","title":"iCount","text":"iCount: protein-RNA interaction analysis is a Python module and associated command-line interface (CLI), which provides all the commands needed to process iCLIP data on protein-RNA interactions.
homepage: https://github.com/tomazc/iCount
version versionsuffix toolchain 20180820 -Python-3.6.6 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/iVar/","title":"iVar","text":"iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
homepage: https://github.com/andersen-lab/ivar
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","boost":0.5},{"location":"version-specific/supported-software/i/icc/","title":"icc","text":"C and C++ compiler from Intel
homepage: https://software.intel.com/en-us/intel-compilers/
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","boost":0.5},{"location":"version-specific/supported-software/i/iccifort/","title":"iccifort","text":"Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL
homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/
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","boost":0.5},{"location":"version-specific/supported-software/i/iccifortcuda/","title":"iccifortcuda","text":"Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit
homepage: <(none)>
version versionsuffix toolchain 2016.10 system 2017.4.196 -GCC-6.4.0-2.28 system 2019a system 2019b system 2020a system 2020b system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/iced/","title":"iced","text":"Implements the ICE normalization of hic data.
homepage: https://github.com/hiclib/iced
version toolchain 0.5.10 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/ichorCNA/","title":"ichorCNA","text":"ichorCNA is a tool for estimating the fraction of tumor in cell-free DNA from ultra-low-pass whole genome sequencing
homepage: https://github.com/broadinstitute/ichorCNA/wiki
version toolchain 0.2.0 foss/2019b 0.3.2-20191219 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/icmake/","title":"icmake","text":"Icmake is a hybrid between a 'make' utility and a 'shell script' language. Originally, it was written to provide a useful tool for automatic program maintenance and system administrative tasks on old MS-DOS platforms.
homepage: http://icmake.sourceforge.net/
version toolchain 7.23.02 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/idemux/","title":"idemux","text":"idemux - inline barcode demultiplexing Idemux is a command line tool designed to demultiplex paired-end FASTQ files from QuantSeq-Pool.
homepage: https://github.com/Lexogen-Tools/idemux
version toolchain 0.1.6 GCCcore/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/ieeg-cli/","title":"ieeg-cli","text":"IEEG.ORG is a collaborative initiative funded by the National Institutes of Neurological Disorders and Stroke. This initiative seeks to advance research towards the understanding of epilepsy by providing a platform for sharing data, tools and expertise between researchers.
homepage: https://www.ieeg.org/
version toolchain 1.14.56 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/ifort/","title":"ifort","text":"Fortran compiler from Intel
homepage: https://software.intel.com/en-us/intel-compilers/
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","boost":0.5},{"location":"version-specific/supported-software/i/igraph/","title":"igraph","text":"igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++.
homepage: https://igraph.org
version toolchain 0.10.10 foss/2023a 0.10.12 foss/2023b 0.10.3 foss/2022a 0.10.6 foss/2022b 0.7.1 foss/2018b 0.7.1 intel/2016b 0.7.1 intel/2017b 0.8.0 foss/2019b 0.8.2 foss/2020a 0.8.5 foss/2020b 0.9.1 foss/2020b 0.9.1 fosscuda/2020b 0.9.4 foss/2021a 0.9.5 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/igv-reports/","title":"igv-reports","text":"Python application to generate self-contained igv.js pages that can be opened within a browser with \"file\" protocol.
homepage: https://github.com/igvteam/igv-reports
version versionsuffix toolchain 0.9.8 -Python-3.7.4 GCC/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/igvShiny/","title":"igvShiny","text":"An htmlwidget version of igv, for RStudio and Shiny apps
homepage: https://github.com/gladkia/igvShiny
version versionsuffix toolchain 20240112 -R-4.2.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/iibff/","title":"iibff","text":"GCC and GFortran based compiler toolchain with OpenMPI, BLIS, libFLAME, ScaLAPACK and FFTW.
homepage: <(none)>
version toolchain 2020b system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/iimkl/","title":"iimkl","text":"Intel C/C++ and Fortran compilers, alongside Intel Math Kernel Library (MKL).
homepage: https://software.intel.com/en-us/intel-cluster-toolkit-compiler/
version toolchain 2018a system 2022a system 2022b system 2023a system 2023b system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/iimpi/","title":"iimpi","text":"Intel C/C++ and Fortran compilers, alongside Intel MPI.
homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/
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","boost":0.5},{"location":"version-specific/supported-software/i/iimpic/","title":"iimpic","text":"Intel C/C++ and Fortran compilers, alongside Intel MPI.
homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/
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","boost":0.5},{"location":"version-specific/supported-software/i/ilastik-napari/","title":"ilastik-napari","text":"Napari plugin for interactive pixel classification.
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version toolchain 0.2.4 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/imagecodecs/","title":"imagecodecs","text":"Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in the tifffile, czifile, zarr, and other scientific image input/output modules.
homepage: https://github.com/cgohlke/imagecodecs
version toolchain 2021.8.26 foss/2020b 2022.9.26 foss/2021a 2022.9.26 foss/2022a 2024.1.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/imageio/","title":"imageio","text":"Imageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, video, volumetric data, and scientific formats.
homepage: https://imageio.github.io
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","boost":0.5},{"location":"version-specific/supported-software/i/imake/","title":"imake","text":"imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems.
homepage: http://www.x.org/
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","boost":0.5},{"location":"version-specific/supported-software/i/imbalanced-learn/","title":"imbalanced-learn","text":"imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance.
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","boost":0.5},{"location":"version-specific/supported-software/i/imgaug/","title":"imgaug","text":"This python library helps you with augmenting images for your machine learning projects. It converts a set of input images into a new, much larger set of slightly altered images.
homepage: https://imgaug.readthedocs.io/en/latest/
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","boost":0.5},{"location":"version-specific/supported-software/i/imkl-FFTW/","title":"imkl-FFTW","text":"FFTW interfaces using Intel oneAPI Math Kernel Library
homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html
version toolchain 2021.4.0 gompi/2021b 2021.4.0 iimpi/2021b 2022.0.1 iimpi/2022.00 2022.1.0 iimpi/2022.05 2022.1.0 iimpi/2022a 2022.2.0 iimpi/2022.09 2022.2.1 iimpi/2022.11 2022.2.1 iimpi/2022b 2023.0.0 iimpi/2022.12 2023.1.0 iimpi/2023.03 2023.1.0 iimpi/2023a 2023.2.0 iimpi/2023.07 2023.2.0 iimpi/2023b 2024.0.0 iimpi/2023.11 2024.2.0 iimpi/2024a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/imkl/","title":"imkl","text":"Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.
homepage: https://software.intel.com/en-us/intel-mkl/
version versionsuffix toolchain 11.2.3.187 gimpi/2.11.5 11.3.0.109 iimpi/2016.00-GCC-4.9.3-2.25 11.3.1.150 iimpi/2016.01-GCC-4.9.3-2.25 11.3.1.150 iimpi/8.1.5-GCC-4.9.3-2.25 11.3.2.181 iimpi/2016.02-GCC-4.9.3-2.25 11.3.2.181 iimpi/2016.02-GCC-5.3.0-2.26 11.3.2.181 pompi/2016.03 11.3.3.210 iimpi/2016.03-GCC-4.9.3-2.25 11.3.3.210 iimpi/2016.03-GCC-5.3.0-2.26 11.3.3.210 iimpi/2016.03-GCC-5.4.0-2.26 11.3.3.210 iimpi/2016b 11.3.3.210 iimpic/2016.10 11.3.3.210 iompi/2016.07 11.3.3.210 iompi/2016.09-GCC-4.9.3-2.25 11.3.3.210 iompi/2016.09-GCC-5.4.0-2.26 11.3.3.210 pompi/2016.04 11.3.3.210 pompi/2016.09 2017.0.098 iimpi/2017.00-GCC-5.4.0-2.26 2017.1.132 gimpi/2017a 2017.1.132 iimpi/2017.01-GCC-5.4.0-2.26 2017.1.132 iimpi/2017a 2017.1.132 iompi/2017.01 2017.1.132 iompi/2017a 2017.2.174 iimpi/2017.02-GCC-6.3.0-2.27 2017.3.196 gompi/2017b 2017.3.196 iimpi/2017b 2017.3.196 iimpic/2017b 2017.3.196 iompi/2017b 2017.4.239 iimpi/2017.09 2018.0.128 iimpi/2018.00 2018.1.163 -serial iccifort/2018.1.163-GCC-6.4.0-2.28 2018.1.163 iimpi/2018.01 2018.1.163 iimpi/2018a 2018.1.163 iompi/2018a 2018.2.199 iimpi/2018.02 2018.2.199 iompi/2018.02 2018.3.222 gimpi/2018b 2018.3.222 gompi/2018b 2018.3.222 iimpi/2018b 2018.3.222 iompi/2018b 2018.4.274 iimpi/2018.04 2019.0.117 iimpi/2019.00 2019.1.144 gompi/2019a 2019.1.144 iimpi/2019.01 2019.1.144 iimpi/2019a 2019.1.144 iimpic/2019a 2019.1.144 iompi/2019.01 2019.2.187 iimpi/2019.02 2019.3.199 iimpi/2019.03 2019.5.281 gompi/2019b 2019.5.281 gompic/2019b 2019.5.281 iimpi/2019b 2019.5.281 iimpic/2019b 2019.5.281 iompi/2019b 2020.0.166 iimpi/2020.00 2020.1.217 gompi/2020a 2020.1.217 iimpi/2020.06-impi-18.5 2020.1.217 iimpi/2020a 2020.1.217 iimpic/2020a 2020.1.217 iompi/2020a 2020.4.304 NVHPC/21.2 2020.4.304 gompi/2020b 2020.4.304 gompic/2020b 2020.4.304 iimpi/2020b 2020.4.304 iimpic/2020b 2020.4.304 iompi/2020b 2021.1.1 iimpi/2020.12 2021.2.0 gompi/2021a 2021.2.0 iimpi/2021a 2021.2.0 iompi/2021a 2021.3.0 gompi/2021a 2021.4.0 iompi/2021b 2021.4.0 system 2022.0.1 system 2022.1.0 gompi/2022a 2022.1.0 system 2022.2.0 system 2022.2.1 system 2023.0.0 system 2023.1.0 gompi/2023a 2023.1.0 system 2023.2.0 system 2024.0.0 system 2024.2.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/immunedeconv/","title":"immunedeconv","text":"immunedeconv is an R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data.
homepage: https://github.com/icbi-lab/immunedeconv
version versionsuffix toolchain 2.0.2 -R-4.0.0 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/impi/","title":"impi","text":"The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.
homepage: https://software.intel.com/en-us/intel-mpi-library/
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","boost":0.5},{"location":"version-specific/supported-software/i/imutils/","title":"imutils","text":"A series of convenience functions to make basic image processing operations such as translation, rotation, resizing, skeletonization, and displaying Matplotlib images easier with OpenCV and Python.
homepage: https://github.com/jrosebr1/imutils
version versionsuffix toolchain 0.5.4 -CUDA-11.7.0 foss/2022a 0.5.4 fosscuda/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/indicators/","title":"indicators","text":" - Thread-safe progress bars and spinners - Header-only library. Grab a copy of include/indicators. - Single-header version in single_include/indicators.
homepage: https://github.com/p-ranav/indicators
version toolchain 2.2 GCCcore/11.2.0 2.2 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/inferCNV/","title":"inferCNV","text":"InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence for somatic large-scale chromosomal copy number alterations, such as gains or deletions of entire chromosomes or large segments of chromosomes.
homepage: https://github.com/broadinstitute/inferCNV/wiki
version versionsuffix toolchain 1.0.4 -Python-3.7.2-R-3.6.0 foss/2019a 1.10.1 -R-4.1.2 foss/2021b 1.12.0 -R-4.2.1 foss/2022a 1.14.2 -R-4.2.2 foss/2022b 1.2.1 -Python-3.7.4 foss/2019b 1.21.0 -R-4.3.2 foss/2023a 1.3.3 -Python-3.8.2 foss/2020a 1.3.3 foss/2020b 1.3.3 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/infercnvpy/","title":"infercnvpy","text":"Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
homepage: https://github.com/icbi-lab/infercnvpy
version toolchain 0.4.0 foss/2021b 0.4.2 foss/2022a 0.4.3 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/inflection/","title":"inflection","text":"inflection is a package that finds the inflection point of a planar curve which is given as a data frame of discrete (xi,yi) points
homepage: https://github.com/dchristop/inflection
version versionsuffix toolchain 1.3.5 -R-4.3.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/inih/","title":"inih","text":"Direct Rendering Manager runtime library.
homepage: https://dri.freedesktop.org
version toolchain 57 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/inline/","title":"inline","text":"Functionality to dynamically define R functions and S4 methods with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling conventions.
homepage: https://cran.r-project.org/web/packages/inline
version versionsuffix toolchain 0.3.19 -R-4.0.4 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/inputproto/","title":"inputproto","text":"X.org InputProto protocol headers.
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 2.3.1 foss/2016a 2.3.1 gimkl/2.11.5 2.3.1 intel/2016a 2.3.2 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/intel-compilers/","title":"intel-compilers","text":"Intel C, C++ & Fortran compilers (classic and oneAPI)
homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html
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","boost":0.5},{"location":"version-specific/supported-software/i/intel/","title":"intel","text":"Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.
homepage: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain
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","boost":0.5},{"location":"version-specific/supported-software/i/intelcuda/","title":"intelcuda","text":"Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit
homepage: <(none)>
version toolchain 2016.10 system 2017b system 2019a system 2019b system 2020a system 2020b system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/intervaltree-python/","title":"intervaltree-python","text":"A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment
homepage: https://github.com/chaimleib/intervaltree
version versionsuffix toolchain 3.0.2 -Python-3.6.6 foss/2018b 3.1.0 GCCcore/10.3.0 3.1.0 GCCcore/11.2.0 3.1.0 GCCcore/11.3.0 3.1.0 GCCcore/12.2.0 3.1.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/intervaltree/","title":"intervaltree","text":"An interval tree can be used to efficiently find a set of numeric intervals overlapping or containing another interval. This library provides a basic implementation of an interval tree using C++ templates, allowing the insertion of arbitrary types into the tree.
homepage: https://github.com/ekg/intervaltree
version toolchain 0.1 GCCcore/10.2.0 0.1 GCCcore/10.3.0 0.1 GCCcore/11.2.0 0.1 GCCcore/11.3.0 0.1 GCCcore/12.2.0 0.1 GCCcore/12.3.0 0.1 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/intltool/","title":"intltool","text":"intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.
homepage: https://freedesktop.org/wiki/Software/intltool/
version versionsuffix toolchain 0.51.0 GCCcore/10.2.0 0.51.0 GCCcore/10.3.0 0.51.0 GCCcore/11.2.0 0.51.0 GCCcore/11.3.0 0.51.0 GCCcore/12.2.0 0.51.0 GCCcore/12.3.0 0.51.0 GCCcore/13.2.0 0.51.0 GCCcore/13.3.0 0.51.0 -Perl-5.24.0 GCCcore/4.9.3 0.51.0 -Perl-5.24.0 GCCcore/5.4.0 0.51.0 -Perl-5.24.1 GCCcore/6.3.0 0.51.0 -Perl-5.26.0 GCCcore/6.4.0 0.51.0 -Perl-5.26.1 GCCcore/6.4.0 0.51.0 -Perl-5.28.0 GCCcore/7.3.0 0.51.0 GCCcore/8.2.0 0.51.0 GCCcore/8.3.0 0.51.0 GCCcore/9.3.0 0.51.0 -Perl-5.22.1 foss/2016a 0.51.0 -Perl-5.24.0 foss/2016b 0.51.0 -Perl-5.24.0 gimkl/2017a 0.51.0 -Perl-5.20.3 intel/2016a 0.51.0 -Perl-5.22.1 intel/2016a 0.51.0 -Perl-5.24.0 intel/2016b 0.51.0 -Perl-5.24.1 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/io_lib/","title":"io_lib","text":"Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a \"Read\" C structure with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows.
homepage: http://sourceforge.net/projects/staden/files/io_lib/
version toolchain 1.14.8 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/ioapi/","title":"ioapi","text":"The Models-3/EDSS Input/Output Applications Programming Interface (I/O API) provides the environmental model developer with an easy-to-learn, easy-to-use programming library for data storage and access, available from both Fortran and C. The same routines can be used for both file storage (using netCDF files) and model coupling (using PVM mailboxes). It is the standard data access library for both the NCSC/CMAS's EDSS project and EPA's Models-3, CMAQ, and SMOKE, as well as various other atmospheric and hydrological modeling systems.
homepage: https://www.cmascenter.org/ioapi/
version versionsuffix toolchain 3.2-2020111 -nocpl gompi/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/iodata/","title":"iodata","text":"Python library for reading, writing, and converting computational chemistry file formats and generating input files.
homepage: https://github.com/theochem/iodata
version toolchain 1.0.0a2 intel/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/iomkl/","title":"iomkl","text":"Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.
homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/
version toolchain 2016.07 system 2016.09-GCC-4.9.3-2.25 system 2016.09-GCC-5.4.0-2.26 system 2017.01 system 2017a system 2017b system 2018.02 system 2018a system 2018b system 2019.01 system 2019b system 2020a system 2020b system 2021a system 2021b system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/iompi/","title":"iompi","text":"Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI.
homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/
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","boost":0.5},{"location":"version-specific/supported-software/i/iperf/","title":"iperf","text":"Iperf 2: TCP and UDP bandwidth performance measurement tool
homepage: https://sourceforge.net/projects/iperf2/
version toolchain 2.1.9 GCCcore/10.2.0 3.15 system 3.16 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/ipp/","title":"ipp","text":"Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms.
homepage: https://software.intel.com/en-us/articles/intel-ipp/
version toolchain 2017.1.132 system 7.0.5.233 system 8.1.0.144 system 9.0.1.150 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/ipympl/","title":"ipympl","text":"Leveraging the Jupyter interactive widgets framework, ipympl enables the interactive features of matplotlib in the Jupyter notebook and in JupyterLab. Besides, the figure canvas element is a proper Jupyter interactive widget which can be positioned in interactive widget layouts.
homepage: https://matplotlib.org/ipympl
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","boost":0.5},{"location":"version-specific/supported-software/i/ipyparallel/","title":"ipyparallel","text":"ipyparallel is a Python package and collection of CLI scripts for controlling clusters for Jupyter
homepage: https://ipyparallel.readthedocs.io
version versionsuffix toolchain 6.2.2 -Python-3.6.4 foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/ipyrad/","title":"ipyrad","text":"ipyrad is an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.
homepage: https://ipyrad.readthedocs.io
version versionsuffix toolchain 0.6.15 -Python-2.7.13 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/irodsfs/","title":"irodsfs","text":"FUSE implementation of iRODS Client written in Golang.
homepage: https://github.com/cyverse/irodsfs
version versionsuffix toolchain 0.8.11 -linux-amd64 system 0.8.12 -linux-amd64 system 0.8.9 -linux-amd64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/isoCirc/","title":"isoCirc","text":"isoCirc: computational pipeline to identify high-confidence BSJs and full-length circRNA isoforms from isoCirc long-read data
homepage: https://github.com/Xinglab/isoCirc
version toolchain 1.0.4 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/i/ispc/","title":"ispc","text":"Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, with extensions for 'single program, multiple data' (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware.
homepage: http://ispc.github.io/ , https://github.com/ispc/ispc/
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","boost":0.5},{"location":"version-specific/supported-software/i/itac/","title":"itac","text":"The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays.
homepage: https://software.intel.com/en-us/intel-trace-analyzer/
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","boost":0.5},{"location":"version-specific/supported-software/i/itpp/","title":"itpp","text":"IT++ is a C++ library of mathematical, signal processing and communication classes and functions. Its main use is in simulation of communication systems and for performing research in the area of communications.
homepage: https://sourceforge.net/projects/itpp/
version toolchain 4.3.1 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/","title":"List of supported software (j)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- JAGS
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- Jmol
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- jupyter-rsession-proxy
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- jupyter-vscode-proxy
- JupyterHub
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(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/JAGS/","title":"JAGS","text":"JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
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","boost":0.5},{"location":"version-specific/supported-software/j/JAXFrontCE/","title":"JAXFrontCE","text":"JAXFront is a technology to generate graphical user interfaces on multiple channels (Java Swing, HTML, PDF) on the basis of an XML schema.
homepage: http://www.jaxfront.org/pages/free_community_edition.html
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","boost":0.5},{"location":"version-specific/supported-software/j/JSON-GLib/","title":"JSON-GLib","text":"JSON-GLib implements a full JSON parser and generator using GLib and GObject, and integrates JSON with GLib data types.
homepage: https://wiki.gnome.org/Projects/JsonGlib
version toolchain 1.6.2 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/JUBE/","title":"JUBE","text":"The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, run those sets on different computer systems and evaluate the results.
homepage: http://www.fz-juelich.de/jsc/jube
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","boost":0.5},{"location":"version-specific/supported-software/j/JUnit/","title":"JUnit","text":"A programmer-oriented testing framework for Java.
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","boost":0.5},{"location":"version-specific/supported-software/j/JWM/","title":"JWM","text":"JWM is a light-weight window manager for the X11 Window System.
homepage: https://joewing.net/projects/jwm/
version toolchain 2.3.5 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/Jansson/","title":"Jansson","text":"Jansson is a C library for encoding, decoding and manipulating JSON data. Its main features and design principles are: * Simple and intuitive API and data model * Comprehensive documentation * No dependencies on other libraries * Full Unicode support (UTF-8) * Extensive test suite
homepage: https://www.digip.org/jansson/
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","boost":0.5},{"location":"version-specific/supported-software/j/JasPer/","title":"JasPer","text":"The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
homepage: http://www.ece.uvic.ca/~frodo/jasper/
version toolchain 1.900.1 GCCcore/5.4.0 1.900.1 GCCcore/6.4.0 1.900.1 GCCcore/8.2.0 1.900.1 foss/2016a 1.900.1 foss/2016b 1.900.1 foss/2017a 1.900.1 intel/2016a 1.900.1 intel/2016b 1.900.1 intel/2017a 2.0.10 intel/2016b 2.0.12 GCCcore/6.4.0 2.0.12 foss/2016b 2.0.12 intel/2017a 2.0.14 GCCcore/6.4.0 2.0.14 GCCcore/7.3.0 2.0.14 GCCcore/8.2.0 2.0.14 GCCcore/8.3.0 2.0.14 GCCcore/9.3.0 2.0.16 GCCcore/9.3.0 2.0.24 GCCcore/10.2.0 2.0.28 GCCcore/10.3.0 2.0.33 GCCcore/11.2.0 2.0.33 GCCcore/11.3.0 4.0.0 GCCcore/12.2.0 4.0.0 GCCcore/12.3.0 4.0.0 GCCcore/13.2.0 4.2.4 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/Jasmine/","title":"Jasmine","text":"SV Merging Across Samples
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","boost":0.5},{"location":"version-specific/supported-software/j/Java/","title":"Java","text":"Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
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","boost":0.5},{"location":"version-specific/supported-software/j/JavaFX/","title":"JavaFX","text":"OpenJFX is an open source, next generation client application platform for desktop, mobile and embedded systems built on Java
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version versionsuffix toolchain 11.0.2 _linux-x64_bin-sdk system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/Jblob/","title":"Jblob","text":"Jblob - WDC Climate dataset download
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version toolchain 3.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/Jellyfish/","title":"Jellyfish","text":"Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
homepage: http://www.cbcb.umd.edu/software/jellyfish/
version toolchain 1.1.11 foss/2016a 1.1.11 foss/2016b 1.1.12 foss/2018b 1.1.12 intel/2018a 2.2.10 foss/2018b 2.2.10 intel/2018a 2.2.6 foss/2016b 2.2.6 intel/2017a 2.3.0 GCC/10.2.0 2.3.0 GCC/10.3.0 2.3.0 GCC/11.2.0 2.3.0 GCC/11.3.0 2.3.0 GCC/12.2.0 2.3.0 GCC/8.2.0-2.31.1 2.3.0 GCC/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/JiTCODE/","title":"JiTCODE","text":"Just-in-time compilation for ordinary/delay/stochastic differential equations (DDEs)
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version versionsuffix toolchain 1.3.2 -Python-3.6.4 intel/2018a 1.4.0 -Python-3.7.2 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/Jmol/","title":"Jmol","text":"Jmol: an open-source Java viewer for chemical structures in 3D
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version versionsuffix toolchain 16.1.41 -Java-11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/Jorg/","title":"Jorg","text":"A MAG Circularization Method By Lauren Lui, Torben Nielsen, and Adam Arkin
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version toolchain 1.0.1 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/JsonCpp/","title":"JsonCpp","text":"JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.
homepage: http://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html
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","boost":0.5},{"location":"version-specific/supported-software/j/Jupyter-bundle/","title":"Jupyter-bundle","text":"This bundle collects a range of Jupyter interfaces (Lab, Notebook and nbclassic), extensions (Jupyter Server Proxy, Jupyter Resource Monitor, Jupyter Lmod) and the JupyterHub.
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","boost":0.5},{"location":"version-specific/supported-software/j/JupyterHub/","title":"JupyterHub","text":"JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs.
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","boost":0.5},{"location":"version-specific/supported-software/j/JupyterNotebook/","title":"JupyterNotebook","text":"The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience.
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version versionsuffix toolchain 2.1.10r20160303 -Java-1.8.0_92 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jax/","title":"jax","text":"Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more
homepage: https://pypi.python.org/pypi/jax
version versionsuffix toolchain 0.2.19 foss/2020b 0.2.19 fosscuda/2020b 0.2.20 foss/2021a 0.2.24 -CUDA-11.3.1 foss/2021a 0.2.24 foss/2021a 0.3.14 -CUDA-11.7.0 foss/2022a 0.3.23 -CUDA-11.4.1 foss/2021b 0.3.23 foss/2022a 0.3.25 -CUDA-11.7.0 foss/2022a 0.3.25 foss/2022a 0.3.9 -CUDA-11.3.1 foss/2021a 0.3.9 foss/2021a 0.4.25 -CUDA-12.1.1 gfbf/2023a 0.4.25 gfbf/2023a 0.4.4 -CUDA-11.7.0 foss/2022a 0.4.4 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jbigkit/","title":"jbigkit","text":"JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents.
homepage: https://www.cl.cam.ac.uk/~mgk25/jbigkit/
version toolchain 2.1 GCCcore/10.2.0 2.1 GCCcore/10.3.0 2.1 GCCcore/11.2.0 2.1 GCCcore/11.3.0 2.1 GCCcore/12.2.0 2.1 GCCcore/12.3.0 2.1 GCCcore/13.2.0 2.1 GCCcore/13.3.0 2.1 GCCcore/7.3.0 2.1 GCCcore/8.2.0 2.1 GCCcore/8.3.0 2.1 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jedi-language-server/","title":"jedi-language-server","text":"A Python Language Server powered by Jedi.
homepage: https://github.com/pappasam/jedi-language-server
version toolchain 0.39.0 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jedi/","title":"jedi","text":"Jedi is a static analysis tool for Python that is typically used in IDEs/editors plugins.
homepage: https://jedi.readthedocs.io/en/latest/
version toolchain 0.18.1 GCCcore/11.3.0 0.19.1 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jemalloc/","title":"jemalloc","text":"jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
homepage: http://www.canonware.com/jemalloc
version toolchain 4.1.0 intel/2016a 4.2.0 foss/2016a 4.2.0 intel/2016a 4.2.1 intel/2016b 4.5.0 intel/2017a 5.0.1 GCCcore/6.4.0 5.1.0 GCCcore/7.3.0 5.2.0 GCCcore/8.2.0 5.2.1 GCCcore/10.2.0 5.2.1 GCCcore/10.3.0 5.2.1 GCCcore/11.2.0 5.2.1 GCCcore/11.3.0 5.2.1 GCCcore/8.3.0 5.2.1 GCCcore/9.3.0 5.3.0 GCCcore/11.3.0 5.3.0 GCCcore/12.2.0 5.3.0 GCCcore/12.3.0 5.3.0 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jhbuild/","title":"jhbuild","text":"JHBuild allows you to automatically download and compile \u201cmodules\u201d (i.e. source code packages). Modules are listed in \u201cmodule set\u201d files, which also include dependency information so that JHBuild can discover what modules need to be built and in what order.
homepage: https://wiki.gnome.org/action/show/Projects/Jhbuild
version toolchain 3.15.92 GCCcore/4.9.3 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jiter/","title":"jiter","text":"Fast iterable JSON parser
homepage: https://github.com/pydantic/jiter/tree/main
version toolchain 0.4.1 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/joypy/","title":"joypy","text":"Joyplots in Python with matplotlib & pandas
homepage: https://github.com/sbebo/joypy
version versionsuffix toolchain 0.2.2 -Python-3.7.4 intel/2019b 0.2.4 intel/2020b 0.2.6 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jq/","title":"jq","text":"jq is a lightweight and flexible command-line JSON processor.
homepage: https://stedolan.github.io/jq/
version toolchain 1.5 GCCcore/10.2.0 1.5 GCCcore/6.4.0 1.6 GCCcore/11.2.0 1.6 GCCcore/11.3.0 1.6 GCCcore/12.2.0 1.6 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/json-c/","title":"json-c","text":"JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects.
homepage: https://github.com/json-c/json-c
version toolchain 0.15 GCCcore/10.2.0 0.15 GCCcore/10.3.0 0.15 GCCcore/11.2.0 0.16 GCCcore/11.3.0 0.16 GCCcore/12.2.0 0.16 GCCcore/12.3.0 0.17 GCCcore/13.2.0 0.17 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/json-fortran/","title":"json-fortran","text":"JSON-Fortran: A Modern Fortran JSON API
homepage: https://github.com/jacobwilliams/json-fortran
version toolchain 8.3.0 GCC/10.2.0 8.3.0 GCC/10.3.0 8.3.0 GCC/11.2.0 8.3.0 GCC/11.3.0 8.3.0 GCC/12.2.0 8.3.0 iccifort/2020.4.304 8.3.0 intel-compilers/2022.0.1 8.3.0 intel-compilers/2022.1.0 8.3.0 intel-compilers/2022.2.1 8.5.2 GCC/13.2.0 8.5.2 intel-compilers/2023.2.1 9.0.2 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/junos-eznc/","title":"junos-eznc","text":"Python library for Junos automation.
homepage: https://github.com/Juniper/py-junos-eznc
version toolchain 2.7.1 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jupyter-collaboration/","title":"jupyter-collaboration","text":"JupyterLab Real-Time Collaboration is a Jupyter Server Extension and JupyterLab extensions providing support for Y documents and adding collaboration UI elements in JupyterLab.
homepage: https://github.com/jupyterlab/jupyter-collaboration
version toolchain 2.1.1 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jupyter-contrib-nbextensions/","title":"jupyter-contrib-nbextensions","text":"A collection of various notebook extensions for Jupyter
homepage: https://github.com/ipython-contrib/jupyter_contrib_nbextensions
version toolchain 0.7.0 GCCcore/11.3.0 0.7.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jupyter-matlab-proxy/","title":"jupyter-matlab-proxy","text":"MATLAB Integration for Jupyter
homepage: https://github.com/mathworks/jupyter-matlab-proxy
version toolchain 0.12.2 GCCcore/12.3.0 0.3.4 GCCcore/10.3.0 0.5.0 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jupyter-resource-usage/","title":"jupyter-resource-usage","text":"Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU)
homepage: https://github.com/jupyter-server/jupyter-resource-usage
version toolchain 0.6.1 GCCcore/10.3.0 0.6.2 GCCcore/10.3.0 0.6.3 GCCcore/11.3.0 1.0.0 GCCcore/12.3.0 1.0.2 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jupyter-rsession-proxy/","title":"jupyter-rsession-proxy","text":"Jupyter extensions for running an RStudio rsession proxy
homepage: https://github.com/jupyterhub/jupyter-rsession-proxy
version toolchain 2.1.0 GCCcore/11.3.0 2.2.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jupyter-server-proxy/","title":"jupyter-server-proxy","text":"Jupyter Server Proxy lets you run arbitrary external processes (such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) alongside your notebook server and provide authenticated web access to them using a path like /rstudio next to others like /lab. Alongside the python package that provides the main functionality, the JupyterLab extension (@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window to get to RStudio for example.
homepage: https://github.com/jupyterhub/jupyter-server-proxy
version toolchain 3.2.1 GCCcore/10.3.0 3.2.2 GCCcore/11.3.0 3.2.2 GCCcore/12.2.0 4.0.0 GCCcore/12.3.0 4.1.2 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jupyter-server/","title":"jupyter-server","text":"The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila.
homepage: https://jupyter.org/
version toolchain 1.21.0 GCCcore/11.3.0 2.14.0 GCCcore/13.2.0 2.7.0 GCCcore/12.2.0 2.7.2 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jupyter-vscode-proxy/","title":"jupyter-vscode-proxy","text":"VS Code extension for Jupyter
homepage: https://github.com/betatim/vscode-binder
version toolchain 0.6 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jupyterlab-lmod/","title":"jupyterlab-lmod","text":"JupyterLab extension that allows user to interact with environment modules before launching kernels. The extension use Lmod's Python interface to accomplish module related task like loading, unloading, saving collection, etc.
homepage: https://github.com/cmd-ntrf/jupyter-lmod
version toolchain 1.0.2 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jupyterlmod/","title":"jupyterlmod","text":"Jupyter interactive notebook server extension that allows user to interact with environment modules before launching kernels. The extension use Lmod's Python interface to accomplish module related task like loading, unloading, saving collection, etc.
homepage: https://github.com/cmd-ntrf/jupyter-lmod
version toolchain 3.0.0 GCCcore/11.3.0 4.0.3 GCCcore/11.3.0 4.0.3 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/j/jxrlib/","title":"jxrlib","text":"Open source implementation of jpegxr
homepage: https://github.com/4creators/jxrlib
version toolchain 1.1 GCCcore/10.2.0 1.1 GCCcore/10.3.0 1.1 GCCcore/11.3.0 1.1 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/","title":"List of supported software (k)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- KaHIP
- Kaiju
- Kaleido
- Kalign
- kallisto
- KAT
- kb-python
- kbproto
- kedro
- Kent_tools
- Keras
- KerasTuner
- khmer
- kim-api
- kineto
- king
- KITE
- kma
- KMC
- KMCP
- KmerGenie
- kneaddata
- KNIME
- kpcalg
- Kraken
- Kraken2
- KrakenUniq
- Kratos
- krbalancing
- KronaTools
- kwant
- KWIML
- kWIP
- KyotoCabinet
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/KAT/","title":"KAT","text":"The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
homepage: https://www.earlham.ac.uk/kat-tools
version versionsuffix toolchain 2.4.2 -Python-3.6.4 foss/2018a 2.4.2 -Python-3.7.2 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/KITE/","title":"KITE","text":"KITE is an open-source Python/C++ software suite for efficient real-space tight-binding (TB) simulations of electronic structure and bulk quantum transport properties of disordered systems scalable to multi billions of atomic orbitals.
homepage: https://github.com/quantum-kite/kite
version toolchain 1.1 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/KMC/","title":"KMC","text":"KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.
homepage: http://sun.aei.polsl.pl/kmc
version versionsuffix toolchain 3.1.0 foss/2018a 3.1.0 foss/2018b 3.1.1 -Python-3.7.2 GCC/8.2.0-2.31.1 3.1.2rc1 -Python-3.7.4 GCC/8.3.0 3.2.1 -Python-2.7.18 GCC/11.2.0 3.2.1 GCC/11.2.0 3.2.2 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/KMCP/","title":"KMCP","text":"KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
homepage: https://bioinf.shenwei.me/kmcp
version toolchain 0.9.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/KNIME/","title":"KNIME","text":"KNIME Analytics Platform is the open source software for creating data science applications and services. KNIME stands for KoNstanz Information MinEr.
homepage: https://www.knime.com/
version toolchain 3.6.2 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/KWIML/","title":"KWIML","text":"The Kitware Information Macro Library
homepage: https://gitlab.kitware.com/utils/kwiml
version toolchain 20180201 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/KaHIP/","title":"KaHIP","text":"The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning.
homepage: https://kahip.github.io/
version toolchain 3.14 gompi/2022a 3.14 gompi/2022b 3.16 gompi/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/Kaiju/","title":"Kaiju","text":"Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments
homepage: http://kaiju.binf.ku.dk/
version versionsuffix toolchain 1.5.0 intel/2016b 1.7.2 -Python-3.7.2 iimpi/2019a 1.7.3 -Python-3.7.4 gompi/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/Kaleido/","title":"Kaleido","text":"Fast static image export for web-based visualization libraries with zero dependencies
homepage: https://github.com/plotly/Kaleido
version toolchain 0.1.0 GCCcore/10.2.0 0.2.1 GCCcore/10.3.0 0.2.1 GCCcore/11.3.0 0.2.1 GCCcore/12.2.0 0.2.1 GCCcore/12.3.0 0.2.1 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/Kalign/","title":"Kalign","text":"Kalign is a fast multiple sequence alignment program for biological sequences.
homepage: https://msa.sbc.su.se/cgi-bin/msa.cgi
version toolchain 2.0.4 GCCcore/10.2.0 3.3.1 GCCcore/10.2.0 3.3.1 GCCcore/10.3.0 3.3.2 GCCcore/11.2.0 3.3.5 GCCcore/11.3.0 3.4.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/Kent_tools/","title":"Kent_tools","text":"Kent tools: collection of tools used by the UCSC genome browser.
homepage: http://genome.cse.ucsc.edu/
version versionsuffix toolchain 20130806 -linux.x86_64 system 20171107 -linux.x86_64 system 20180716 -linux.x86_64 system 20190326 -linux.x86_64 system 401 gompi/2019b 411 GCC/10.2.0 418 GCC/10.3.0 422 GCC/11.2.0 442 GCC/11.3.0 457 GCC/12.2.0 461 GCC/12.2.0 468 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/Keras/","title":"Keras","text":"Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano.
homepage: https://keras.io/
version versionsuffix toolchain 1.0.8 -Python-3.5.2 intel/2016b 1.1.0 -Python-3.5.2 intel/2016b 2.0.4 -Python-2.7.13 intel/2017a 2.0.4 -Python-3.6.1 intel/2017a 2.0.5 -Python-3.6.1 intel/2017a 2.0.8 -Python-3.6.1 intel/2017a 2.1.1 -Python-2.7.14 intel/2017b 2.1.1 -Python-3.6.3 intel/2017b 2.1.2 -Python-3.6.3 foss/2017b 2.1.2 -Python-2.7.14 intel/2017b 2.1.3 -Python-3.6.3 foss/2017b 2.1.3 -Python-3.6.3 intel/2017b 2.2.0 -Python-3.6.4 foss/2018a 2.2.0 -Python-2.7.14 fosscuda/2017b 2.2.0 -Python-3.6.3 fosscuda/2017b 2.2.2 -Python-2.7.15 fosscuda/2018b 2.2.4 -Python-3.6.6 foss/2018b 2.2.4 -Python-3.7.2 foss/2019a 2.2.4 -Python-3.6.6 fosscuda/2018b 2.2.4 -Python-3.7.2 fosscuda/2019a 2.2.4 -Python-3.6.4 intel/2018a 2.3.1 -Python-3.7.4 foss/2019b 2.3.1 -Python-3.8.2 foss/2020a 2.3.1 -Python-3.7.4 fosscuda/2019b 2.4.3 foss/2020b 2.4.3 -TensorFlow-2.5.0 fosscuda/2020b 2.4.3 fosscuda/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/KerasTuner/","title":"KerasTuner","text":"KerasTuner is an easy-to-use, scalable hyperparameter optimization framework that solves the pain points of hyperparameter search.
homepage: https://keras.io/keras_tuner
version toolchain 1.3.5 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/KmerGenie/","title":"KmerGenie","text":"KmerGenie estimates the best k-mer length for genome de novo assembly.
homepage: http://kmergenie.bx.psu.edu/
version toolchain 1.7044 intel/2017a 1.7048 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/Kraken/","title":"Kraken","text":"Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.
homepage: http://ccb.jhu.edu/software/kraken/
version versionsuffix toolchain 0.10.5-beta -Perl-5.22.1 foss/2016a 0.10.5-beta -Perl-5.24.0 foss/2016b 1.0 -Perl-5.26.1 intel/2018a 1.1 -Perl-5.28.0 foss/2018b 1.1.1 GCCcore/10.2.0 1.1.1 GCCcore/10.3.0 1.1.1 GCCcore/11.3.0 1.1.1 -Perl-5.28.1 GCCcore/8.2.0 1.1.1 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/Kraken2/","title":"Kraken2","text":"Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.
homepage: http://ccb.jhu.edu/software/kraken/
version versionsuffix toolchain 2.0.6-beta -Perl-5.26.1 foss/2018a 2.0.7-beta -Perl-5.28.0 foss/2018b 2.0.8-beta -Perl-5.30.0 gompi/2019b 2.0.9-beta -Perl-5.28.0 foss/2018b 2.0.9-beta -Perl-5.30.2 gompi/2020a 2.1.1 gompi/2020b 2.1.2 gompi/2021a 2.1.2 gompi/2021b 2.1.2 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/KrakenUniq/","title":"KrakenUniq","text":"KrakenUniq: confident and fast metagenomics classification using unique k-mer counts
homepage: https://github.com/fbreitwieser/krakenuniq/
version toolchain 1.0.3 GCC/11.3.0 1.0.4 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/Kratos/","title":"Kratos","text":"Kratos Multiphysics (A.K.A Kratos) is a framework for building parallel multi-disciplinary simulation software.
homepage: http://www.cimne.com/kratos
version versionsuffix toolchain 6.0 -Python-3.6.4 foss/2018a 6.0 -Python-3.6.4 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/KronaTools/","title":"KronaTools","text":"Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
homepage: https://github.com/marbl/Krona/wiki/KronaTools
version toolchain 2.7 GCCcore/7.3.0 2.7.1 GCCcore/8.2.0 2.8 GCC/10.3.0 2.8 GCCcore/10.2.0 2.8.1 GCCcore/11.2.0 2.8.1 GCCcore/11.3.0 2.8.1 GCCcore/12.2.0 2.8.1 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/KyotoCabinet/","title":"KyotoCabinet","text":"Kyoto Cabinet is a library of routines for managing a database.
homepage: https://fallabs.com/kyotocabinet
version toolchain 1.2.77 GCCcore/7.3.0 1.2.77 GCCcore/8.2.0 1.2.80 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/kWIP/","title":"kWIP","text":"This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any reference genome, and without assembling one.
homepage: https://github.com/kdmurray91/kWIP
version toolchain 0.2.0 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/kallisto/","title":"kallisto","text":"kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
homepage: http://pachterlab.github.io/kallisto/
version toolchain 0.42.5 foss/2016a 0.43.0 intel/2016b 0.43.1 foss/2016b 0.43.1 intel/2017a 0.43.1 intel/2017b 0.44.0 foss/2016b 0.44.0 intel/2018a 0.45.0 foss/2018b 0.45.1 foss/2019a 0.46.0 intel/2019a 0.46.1 foss/2019b 0.46.1 iimpi/2020a 0.46.1 iimpi/2020b 0.46.2 foss/2020b 0.48.0 gompi/2021a 0.48.0 gompi/2021b 0.48.0 gompi/2022a 0.50.1 gompi/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/kb-python/","title":"kb-python","text":"kallisto | bustools is a workflow for pre-processing single-cell RNA-seq data. Pre-processing single-cell RNA-seq involves: (1) association of reads with their cells of origin, (2) collapsing of reads according to unique molecular identifiers (UMIs), and (3) generation of gene or feature counts from the reads to generate a cell x gene matrix.
homepage: https://www.kallistobus.tools/
version toolchain 0.27.3 foss/2021b 0.27.3 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/kbproto/","title":"kbproto","text":"X.org KBProto protocol headers.
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.0.7 foss/2016a 1.0.7 gimkl/2.11.5 1.0.7 intel/2016a 1.0.7 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/kedro/","title":"kedro","text":"Kedro is an open-source Python framework that applies software engineering best-practice to data and machine-learning pipelines.
homepage: https://github.com/quantumblacklabs/kedro
version versionsuffix toolchain 0.16.5 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/khmer/","title":"khmer","text":"In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
homepage: https://github.com/ged-lab/khmer/
version versionsuffix toolchain 1.4.1 -Python-2.7.12 foss/2016b 2.1.1 -Python-2.7.13 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/kim-api/","title":"kim-api","text":"Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all.
homepage: https://openkim.org/
version toolchain 2.1.2 foss/2019a 2.1.2 intel/2019a 2.1.3 foss/2019b 2.1.3 foss/2020a 2.1.3 intel/2019b 2.1.3 intel/2020a 2.2.1 GCC/10.2.0 2.2.1 GCC/10.3.0 2.2.1 iccifort/2020.4.304 2.3.0 GCC/11.2.0 2.3.0 GCC/11.3.0 2.3.0 GCC/12.2.0 2.3.0 GCC/12.3.0 2.3.0 intel-compilers/2023.1.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/kineto/","title":"kineto","text":"A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters
homepage: https://github.com/pytorch/kineto
version toolchain 0.4.0 GCC/11.3.0 0.4.0 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/king/","title":"king","text":"KING is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequencing project. Applications of KING include family relationship inference and pedigree error checking, quality control, population substructure identification, forensics, gene mapping, etc.
homepage: https://kingrelatedness.com/
version toolchain 2.2.4 system 2.2.7 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/kma/","title":"kma","text":"KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.
homepage: https://bitbucket.org/genomicepidemiology/kma
version toolchain 1.2.22 intel/2019b 1.4.12a GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/kneaddata/","title":"kneaddata","text":"KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
homepage: http://huttenhower.sph.harvard.edu/kneaddata
version toolchain 0.12.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/kpcalg/","title":"kpcalg","text":"Kernel PC (kPC) algorithm for causal structure learning and causal inference using graphical models. kPC is a version of PC algorithm that uses kernel based independence criteria in order to be able to deal with non-linear relationships and non-Gaussian noise. Includes pcalg: Functions for causal structure learning and causal inference using graphical models.
homepage: https://cran.r-project.org/package=kpcalg
version versionsuffix toolchain 1.0.1 -R-3.5.1 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/krbalancing/","title":"krbalancing","text":"A C++ extension for Python which computes K.R. balanced matrices.
homepage: https://github.com/deeptools/Knight-Ruiz-Matrix-balancing-algorithm
version toolchain 0.5.0b0 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/k/kwant/","title":"kwant","text":"Kwant is a free (open source), powerful, and easy to use Python package for numerical calculations on tight-binding models with a strong focus on quantum transport.
homepage: https://kwant-project.org/
version versionsuffix toolchain 1.4.1 -Python-3.7.2 foss/2019a 1.4.1 -Python-3.7.2 intel/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/","title":"List of supported software (l)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- L_RNA_scaffolder
- Lab-Streaming-Layer
- Lace
- LADR
- lagrangian-filtering
- LAME
- LAMMPS
- lancet
- LangChain
- langchain-anthropic
- langchain-mistralai
- langchain-openai
- LAPACK
- LASSO-Python
- LAST
- LASTZ
- lavaan
- LayoutParser
- LBFGS++
- lcalc
- LCov
- LDC
- lDDT
- LeadIT
- leafcutter
- leidenalg
- LEMON
- Leptonica
- LERC
- less
- LevelDB
- Levenshtein
- lftp
- LHAPDF
- LIANA
- libabigail
- libaec
- libaed2
- libaio
- libarchive
- libav
- libavif
- libbaseencode
- libBigWig
- libbitmask
- libbraiding
- libcdms
- libcerf
- libcint
- libcircle
- libcmaes
- libconfig
- libcotp
- libcpuset
- libcroco
- libctl
- libdap
- libde265
- libdeflate
- libdivsufsort
- libdrm
- libdrs
- libdwarf
- libedit
- libelf
- libemf
- libepoxy
- libev
- libevent
- libexif
- libfabric
- libfdf
- libffcall
- libffi
- libFLAME
- libfontenc
- libfyaml
- libgcrypt
- libgd
- libgdiplus
- libGDSII
- libgeotiff
- libgit2
- libglade
- libGLU
- libglvnd
- libgpg-error
- libgpuarray
- libGridXC
- libgtextutils
- libgxps
- libhandy
- libharu
- libheif
- libhomfly
- libibmad
- libibumad
- libICE
- libiconv
- libidn
- libidn2
- Libint
- LiBis
- libjpeg-turbo
- libjxl
- libleidenalg
- LibLZF
- libmad
- libmatheval
- libmaus2
- libmbd
- libMemcached
- libmicrohttpd
- libmo_unpack
- libmypaint
- libnsl
- libobjcryst
- libogg
- libopus
- libosmium
- libpci
- libpciaccess
- libplinkio
- libpng
- libpsl
- libPSML
- libpsortb
- libpspio
- libpthread-stubs
- libQGLViewer
- libreadline
- libRmath
- librosa
- librsb
- librsvg
- librttopo
- libsamplerate
- libSBML
- libsigc++
- libsigsegv
- libSM
- libsndfile
- libsodium
- LibSoup
- libspatialindex
- libspatialite
- libspectre
- libssh
- libStatGen
- libsupermesh
- LIBSVM
- LIBSVM-MATLAB
- LIBSVM-Python
- libtar
- libtasn1
- libtecla
- LibTIFF
- libtirpc
- libtool
- libtree
- libunistring
- libunwind
- libutempter
- LibUUID
- libuv
- libvdwxc
- libvorbis
- libvori
- libWallModelledLES
- libwebp
- libwpe
- libX11
- libXau
- libxc
- libxcb
- libXcursor
- libXdamage
- libXdmcp
- libXext
- libXfixes
- libXfont
- libXft
- libXi
- libXinerama
- libxkbcommon
- libxml++
- libxml2
- libxml2-python
- libXmu
- libXp
- libXpm
- libXrandr
- libXrender
- libxslt
- libxsmm
- libXt
- libXxf86vm
- libyaml
- libzeep
- libzip
- lie_learn
- lifelines
- Lighter
- Lightning
- liknorm
- likwid
- lil-aretomo
- limix
- LinBox
- line_profiler
- Lingeling
- LISFLOOD-FP
- lit
- LittleCMS
- LLDB
- LLVM
- LMDB
- LMfit
- Lmod
- lmoments3
- LncLOOM
- LocARNA
- LoFreq
- Log-Log4perl
- logaddexp
- LOHHLA
- Loki
- longestrunsubsequence
- longread_umi
- Longshot
- loompy
- loomR
- LoopTools
- LoRDEC
- LPeg
- LPJmL
- lpsolve
- LRBinner
- lrcalc
- lrslib
- LS-PrePost
- LSD2
- LSMS
- LTR_retriever
- LtrDetector
- Lua
- LuaJIT
- LuaJIT2-OpenResty
- LuaRocks
- Lucene-Geo-Gazetteer
- LUMPY
- LUSCUS
- lwgrp
- lxml
- lynx
- lz4
- LZO
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LADR/","title":"LADR","text":"Prover9, Mace4, and several related programs come packaged in a system called LADR (Library for Automated Deduction Research).
homepage: https://www.cs.unm.edu/~mccune/mace4/download
version toolchain 2009-11A GCCcore/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LAME/","title":"LAME","text":"LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
homepage: http://lame.sourceforge.net/
version toolchain 3.100 GCCcore/10.2.0 3.100 GCCcore/10.3.0 3.100 GCCcore/11.2.0 3.100 GCCcore/11.3.0 3.100 GCCcore/12.2.0 3.100 GCCcore/12.3.0 3.100 GCCcore/13.2.0 3.100 GCCcore/13.3.0 3.100 GCCcore/6.4.0 3.100 GCCcore/7.3.0 3.100 GCCcore/8.2.0 3.100 GCCcore/8.3.0 3.100 GCCcore/9.3.0 3.100 intel/2017b 3.99.5 foss/2016b 3.99.5 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LAMMPS/","title":"LAMMPS","text":"LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.
homepage: https://www.lammps.org
version versionsuffix toolchain 23Jun2022 -kokkos-CUDA-11.3.1 foss/2021a 23Jun2022 -kokkos foss/2021a 23Jun2022 -kokkos-CUDA-11.4.1 foss/2021b 23Jun2022 -kokkos foss/2021b 23Jun2022 -kokkos foss/2022a 2Aug2023_update2 -kokkos-CUDA-12.1.1 foss/2023a 2Aug2023_update2 -kokkos foss/2023a 3Mar2020 -Python-3.7.4-kokkos foss/2019b 3Mar2020 -Python-3.8.2-kokkos foss/2020a 3Mar2020 -Python-3.7.4-kokkos intel/2019b 3Mar2020 -Python-3.8.2-kokkos intel/2020a 7Aug2019 -Python-3.7.4-kokkos foss/2019b 7Aug2019 -Python-3.7.4-kokkos-OCTP intel/2019b 7Aug2019 -Python-3.7.4-kokkos intel/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LAPACK/","title":"LAPACK","text":"LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.
homepage: https://www.netlib.org/lapack/
version toolchain 3.10.1 GCC/11.2.0 3.10.1 GCC/11.3.0 3.12.0 GCC/12.3.0 3.12.0 GCC/13.2.0 3.8.0 GCC/7.3.0-2.30 3.9.1 GCC/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LASSO-Python/","title":"LASSO-Python","text":"This python library is designed for general purpose usage in the field of Computer Aided Engineering (CAE). It's name originates from the original initiator and donator of the project Lasso GmbH. The library is now maintained by an open-source community.
homepage: https://open-lasso-python.github.io/lasso-python/
version toolchain 2.0.0 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LAST/","title":"LAST","text":"LAST finds similar regions between sequences.
homepage: http://last.cbrc.jp/
version toolchain 1045 intel/2019b 1179 GCC/10.2.0 869 intel/2017a 914 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LASTZ/","title":"LASTZ","text":"LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.
homepage: https://www.bx.psu.edu/~rsharris/lastz/
version toolchain 1.02.00 GCCcore/8.2.0 1.02.00 foss/2016a 1.04.03 foss/2019b 1.04.22 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LBFGS%2B%2B/","title":"LBFGS++","text":"A header-only C++ library for L-BFGS and L-BFGS-B algorithms
homepage: https://lbfgspp.statr.me
version toolchain 0.1.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LCov/","title":"LCov","text":"LCOV - the LTP GCOV extension
homepage: http://ltp.sourceforge.net/coverage/lcov.php
version toolchain 1.13 GCCcore/7.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LDC/","title":"LDC","text":"The LLVM-based D Compiler
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","boost":0.5},{"location":"version-specific/supported-software/l/LEMON/","title":"LEMON","text":"LEMON stands for Library for Efficient Modeling and Optimization in Networks. It is a C++ template library providing efficient implementations of common data structures and algorithms with focus on combinatorial optimization tasks connected mainly with graphs and networks.
homepage: https://lemon.cs.elte.hu
version toolchain 1.3.1 GCC/8.2.0-2.31.1 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LERC/","title":"LERC","text":"LERC is an open-source image or raster format which supports rapid encoding and decoding for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, so the precision of the original input image is preserved (within user defined error bounds).
homepage: https://github.com/Esri/lerc
version toolchain 3.0 GCCcore/10.2.0 3.0 GCCcore/10.3.0 4.0.0 GCCcore/11.3.0 4.0.0 GCCcore/12.2.0 4.0.0 GCCcore/12.3.0 4.0.0 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LHAPDF/","title":"LHAPDF","text":"Les Houches Parton Density Function LHAPDF is the standard tool for evaluating parton distribution functions (PDFs) in high-energy physics.
homepage: http://lhapdf.hepforge.org/
version toolchain 6.5.3 GCC/11.3.0 6.5.4 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LIANA/","title":"LIANA","text":"LIANA: a LIgand-receptor ANalysis frAmework. LIANA enables the use of any combination of ligand-receptor methods and resources, and their consensus.
homepage: https://saezlab.github.io/liana/
version versionsuffix toolchain 0.1.11 -R-4.2.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LIBSVM-MATLAB/","title":"LIBSVM-MATLAB","text":"MATLAB interface of LIBSVM, an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.
homepage: https://www.csie.ntu.edu.tw/~cjlin/libsvm/
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","boost":0.5},{"location":"version-specific/supported-software/l/LIBSVM-Python/","title":"LIBSVM-Python","text":"This tool provides a simple Python interface to LIBSVM, a library for support vector machines (http://www.csie.ntu.edu.tw/~cjlin/libsvm). The interface is very easy to use as the usage is the same as that of LIBSVM. The interface is developed with the built-in Python library \"ctypes\".
homepage: https://pypi.org/project/libsvm-official/
version toolchain 3.30 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LIBSVM/","title":"LIBSVM","text":"LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.
homepage: http://www.csie.ntu.edu.tw/~cjlin/libsvm/
version toolchain 3.22 intel/2016b 3.22 intel/2017b 3.23 foss/2018b 3.23 intel/2018b 3.24 GCCcore/9.3.0 3.25 GCCcore/10.2.0 3.25 GCCcore/10.3.0 3.25 GCCcore/11.2.0 3.30 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LISFLOOD-FP/","title":"LISFLOOD-FP","text":"The LISFLOOD-FP is a raster-based hydrodynamic model originally developed by the University of Bristol. It has undergone extensive development since conception and includes a collection of numerical schemes implemented to solve a variety of mathematical approximations of the 2D shallow water equations of different complexity. The local inertia solver, known as the ACC solver, is widely used to simulate floods with gradually-varying, subcritical flow over sufficiently rough surfaces with Manning\u2019s coefficient of at least 0.03. It has a version with CPU-specific optimisations and enhanced with a subgrid channel model. LISFLOOD-FP also includes second-order discontinuous Galerkin (DG2) and first-order finite volume (FV1) solvers of the full shallow water equations for modelling a wide range of flows, including rapidly-propagating, supercritical flows, shock waves, or flows over very smooth surfaces. The DG2/FV1 solvers are parallelised for the multi-core CPU architecture, but do not integrate with the subgrid channel model nor with the CPU-specific optimisations.
homepage: https://www.seamlesswave.com/LISFLOOD8.0.html
version versionsuffix toolchain 8.1 -CUDA-11.7.0 gompi/2022a 8.1 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LLDB/","title":"LLDB","text":"The debugger component of the LLVM project
homepage: https://lldb.llvm.org/
version versionsuffix toolchain 11.0.0 -Python-3.8.2 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LLVM/","title":"LLVM","text":"The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation (\"LLVM IR\"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.
homepage: https://llvm.org/
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","boost":0.5},{"location":"version-specific/supported-software/l/LMDB/","title":"LMDB","text":"OpenLDAP's Lightning Memory-Mapped Database (LMDB) library.
homepage: https://github.com/LMDB/lmdb
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","boost":0.5},{"location":"version-specific/supported-software/l/LMfit/","title":"LMfit","text":"Lmfit provides a high-level interface to non-linear optimization and curve fitting problems for Python
homepage: https://lmfit.github.io/lmfit-py
version versionsuffix toolchain 0.9.14 -Python-2.7.15 intel/2018b 0.9.9 -Python-3.6.4 intel/2018a 1.0.0 -Python-3.7.4 foss/2019b 1.0.0 -Python-3.7.4 intel/2019b 1.0.1 -Python-3.8.2 foss/2020a 1.0.2 foss/2020b 1.0.2 intel/2020b 1.0.3 foss/2021a 1.0.3 foss/2022a 1.0.3 intel/2022a 1.2.1 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LOHHLA/","title":"LOHHLA","text":"LOHHLA, Loss Of Heterozygosity in Human Leukocyte Antigen, a computational tool to evaluate HLA loss using next-generation sequencing data.
homepage: https://bitbucket.org/mcgranahanlab/lohhla
version versionsuffix toolchain 2018.11.05 -R-3.5.1 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LPJmL/","title":"LPJmL","text":"Dynamic global vegetation model with managed land and river routing
homepage: https://github.com/PIK-LPJmL/LPJmL
version toolchain 4.0.003 iimpi/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LPeg/","title":"LPeg","text":"LPeg is a new pattern-matching library for Lua, based on Parsing Expression Grammars (PEGs).
homepage: http://www.inf.puc-rio.br/~roberto/lpeg/
version toolchain 1.0.2 GCCcore/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LRBinner/","title":"LRBinner","text":"LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB.
homepage: https://github.com/anuradhawick/LRBinner
version toolchain 0.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LS-PrePost/","title":"LS-PrePost","text":"LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA.
homepage: http://lstc.com/products/ls-prepost
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","boost":0.5},{"location":"version-specific/supported-software/l/LSD2/","title":"LSD2","text":"Least-squares methods to estimate rates and dates from phylogenies
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version toolchain 1.9.7 GCCcore/9.3.0 2.2 GCCcore/10.2.0 2.3 GCCcore/10.3.0 2.3 GCCcore/11.2.0 2.3 GCCcore/11.3.0 2.4.1 GCCcore/12.2.0 2.4.1 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LSMS/","title":"LSMS","text":"LSMS benchmark, part of CORAL suite
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version toolchain 3_rev237 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LTR_retriever/","title":"LTR_retriever","text":"LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
homepage: https://github.com/oushujun/LTR_retriever
version toolchain 2.9.0 foss/2020b 2.9.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LUMPY/","title":"LUMPY","text":"A probabilistic framework for structural variant discovery.
homepage: https://github.com/arq5x/lumpy-sv
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","boost":0.5},{"location":"version-specific/supported-software/l/LUSCUS/","title":"LUSCUS","text":"Luscus is the program for graphical display and editing of molecular systems.
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version toolchain 0.8.6 foss/2018b 0.8.6 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LZO/","title":"LZO","text":"LZO-2.06: Portable lossless data compression library
homepage: http://www.oberhumer.com/opensource/lzo/
version toolchain 2.09 intel/2016b 2.09 intel/2017b 2.10 GCCcore/10.2.0 2.10 GCCcore/10.3.0 2.10 GCCcore/11.2.0 2.10 GCCcore/11.3.0 2.10 GCCcore/12.2.0 2.10 GCCcore/12.3.0 2.10 GCCcore/13.2.0 2.10 GCCcore/13.3.0 2.10 GCCcore/6.4.0 2.10 GCCcore/7.3.0 2.10 GCCcore/8.2.0 2.10 GCCcore/8.3.0 2.10 GCCcore/9.3.0 2.10 foss/2016a 2.10 foss/2016b 2.10 foss/2017a 2.10 foss/2018a 2.10 foss/2018b 2.10 fosscuda/2018b 2.10 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/L_RNA_scaffolder/","title":"L_RNA_scaffolder","text":"L_RNA_scaffolder is a novel scaffolding tool using long trancriptome reads to scaffold genome fragments
homepage: http://www.fishbrowser.org/software/L_RNA_scaffolder/
version versionsuffix toolchain 20141124 -Perl-5.24.0 intel/2016b 20190530 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/Lab-Streaming-Layer/","title":"Lab-Streaming-Layer","text":"The lab streaming layer (LSL) is a system for the unified collection of measurement time series in research experiments that handles both the networking, time-synchronization, (near-) real-time access as well as optionally the centralized collection, viewing and disk recording of the data.
homepage: https://labstreaminglayer.readthedocs.io
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","boost":0.5},{"location":"version-specific/supported-software/l/Lace/","title":"Lace","text":"Building SuperTranscripts: A linear representation of transcriptome data
homepage: https://github.com/Oshlack/Lace
version toolchain 1.14.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LangChain/","title":"LangChain","text":"LangChain is a framework for developing applications powered by large language models (LLMs).
homepage: https://github.com/langchain-ai/langchain
version toolchain 0.2.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LayoutParser/","title":"LayoutParser","text":"A Unified Toolkit for Deep Learning Based Document Image Analysis
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","boost":0.5},{"location":"version-specific/supported-software/l/LeadIT/","title":"LeadIT","text":"Visually Informed LeadOpt
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","boost":0.5},{"location":"version-specific/supported-software/l/Leptonica/","title":"Leptonica","text":"Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications.
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","boost":0.5},{"location":"version-specific/supported-software/l/LevelDB/","title":"LevelDB","text":"LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.
homepage: https://github.com/google/leveldb
version toolchain 1.18 foss/2016a 1.18 intel/2017a 1.18 intel/2017b 1.20 GCCcore/7.3.0 1.22 GCCcore/11.3.0 1.22 GCCcore/8.2.0 1.22 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/Levenshtein/","title":"Levenshtein","text":"Python extension for computing string edit distances and similarities.
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","boost":0.5},{"location":"version-specific/supported-software/l/LiBis/","title":"LiBis","text":"An ultrasensitive alignment method for low input bisulfite sequencing
homepage: https://github.com/Dangertrip/LiBis
version versionsuffix toolchain 20200428 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LibLZF/","title":"LibLZF","text":"LibLZF is a very small data compression library. It consists of only two .c and two .h files and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still written in portable C.
homepage: http://oldhome.schmorp.de/marc/liblzf.html
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","boost":0.5},{"location":"version-specific/supported-software/l/LibSoup/","title":"LibSoup","text":"libsoup is an HTTP client/server library for GNOME. It uses GObjects and the glib main loop, to integrate well with GNOME applications, and also has a synchronous API, for use in threaded applications.
homepage: https://wiki.gnome.org/Projects/libsoup
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","boost":0.5},{"location":"version-specific/supported-software/l/LibTIFF/","title":"LibTIFF","text":"tiff: Library and tools for reading and writing TIFF data files
homepage: https://www.remotesensing.org/libtiff/
version toolchain 4.0.10 GCCcore/8.2.0 4.0.10 GCCcore/8.3.0 4.0.6 GCCcore/5.4.0 4.0.6 foss/2016a 4.0.6 foss/2016b 4.0.6 intel/2016a 4.0.6 intel/2016b 4.0.7 foss/2016b 4.0.7 intel/2017a 4.0.8 intel/2017a 4.0.8 intel/2017b 4.0.9 GCCcore/6.4.0 4.0.9 GCCcore/7.3.0 4.0.9 foss/2017b 4.0.9 intel/2017b 4.0.9 intel/2018.01 4.0.9 intel/2018b 4.1.0 GCCcore/10.2.0 4.1.0 GCCcore/8.3.0 4.1.0 GCCcore/9.3.0 4.2.0 GCCcore/10.3.0 4.3.0 GCCcore/11.2.0 4.3.0 GCCcore/11.3.0 4.4.0 GCCcore/12.2.0 4.5.0 GCCcore/12.3.0 4.6.0 GCCcore/13.2.0 4.6.0 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LibUUID/","title":"LibUUID","text":"Portable uuid C library
homepage: http://sourceforge.net/projects/libuuid/
version toolchain 1.0.3 GCCcore/6.4.0 1.0.3 GCCcore/7.3.0 1.0.3 GCCcore/8.2.0 1.0.3 GCCcore/8.3.0 1.0.3 foss/2016a 1.0.3 intel/2017a 1.0.3 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/Libint/","title":"Libint","text":"Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.
homepage: https://sourceforge.net/p/libint/
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","boost":0.5},{"location":"version-specific/supported-software/l/Lightning/","title":"Lightning","text":"The deep learning framework to pretrain, finetune and deploy AI models. Lightning has 4 core packages: PyTorch Lightning: Train and deploy PyTorch at scale. Lightning Fabric: Expert control. Lightning Data: Blazing fast, distributed streaming of training data from cloud storage. Lightning Apps: Build AI products and ML workflows.
homepage: https://github.com/Lightning-AI/pytorch-lightning
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","boost":0.5},{"location":"version-specific/supported-software/l/Lingeling/","title":"Lingeling","text":"One of the design principles of the state-of-the-art SAT solver Lingeling is to use as compact data structures as possible. These reduce memory usage, increase cache efficiency and thus improve runtime, particularly, when using multiple solver instances on multi-core machines, as in our parallel portfolio solver Plingeling and our cube and conquer solver Treengeling.
homepage: http://fmv.jku.at/lingeling/
version toolchain bcp GCC/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/LittleCMS/","title":"LittleCMS","text":"Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.
homepage: https://www.littlecms.com/
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","boost":0.5},{"location":"version-specific/supported-software/l/Lmod/","title":"Lmod","text":"Lmod is a Lua based module system. Modules allow for dynamic modification of a user's environment under Unix systems. See www.tacc.utexas.edu/tacc-projects/lmod for a complete description. Lmod is a new implementation that easily handles the MODULEPATH Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly.
homepage: http://sourceforge.net/projects/lmod/
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","boost":0.5},{"location":"version-specific/supported-software/l/LncLOOM/","title":"LncLOOM","text":"LncLOOM is a graph-based framework that uses integer programming to identify combinations of short motifs that are deeply conserved in rapidly evolving sequences.
homepage: https://github.com/lncLOOM/lncLOOMv2/
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","boost":0.5},{"location":"version-specific/supported-software/l/LoFreq/","title":"LoFreq","text":"Fast and sensitive variant calling from next-gen sequencing data
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homepage: https://www.lirmm.fr/~rivals/lordec
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","boost":0.5},{"location":"version-specific/supported-software/l/LocARNA/","title":"LocARNA","text":"LocARNA is a collection of alignment tools for the structural analysis of RNA. Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment and is in particular suited for analyzing sets of related RNAs without known common structure.
homepage: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
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","boost":0.5},{"location":"version-specific/supported-software/l/Loki/","title":"Loki","text":"Loki is a C++ library of designs, containing flexible implementations of common design patterns and idioms.
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","boost":0.5},{"location":"version-specific/supported-software/l/Longshot/","title":"Longshot","text":"Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).
homepage: https://github.com/pjedge/longshot
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","boost":0.5},{"location":"version-specific/supported-software/l/LoopTools/","title":"LoopTools","text":"LoopTools is a package for evaluation of scalar and tensor one-loop integrals. It is based on the FF package by G.J. van Oldenborgh.
homepage: https://feynarts.de/looptools/
version toolchain 2.15 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://github.com/TulsaBioinformaticsToolsmith/LtrDetector
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","boost":0.5},{"location":"version-specific/supported-software/l/Lua/","title":"Lua","text":"Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.
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","boost":0.5},{"location":"version-specific/supported-software/l/LuaJIT/","title":"LuaJIT","text":"LuaJIT is a Just-In-Time Compiler (JIT) for the Lua programming language. Lua is a powerful, dynamic and light-weight programming language. It may be embedded or used as a general-purpose, stand-alone language.
homepage: http://luajit.org/
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","boost":0.5},{"location":"version-specific/supported-software/l/LuaJIT2-OpenResty/","title":"LuaJIT2-OpenResty","text":"openresty/luajit2 - OpenResty's maintained branch of LuaJIT. LuaJIT is a Just-In-Time Compiler (JIT) for the Lua programming language. Lua is a powerful, dynamic and light-weight programming language. It may be embedded or used as a general-purpose, stand-alone language.
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homepage: https://luarocks.org
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","boost":0.5},{"location":"version-specific/supported-software/l/Lucene-Geo-Gazetteer/","title":"Lucene-Geo-Gazetteer","text":"A command line gazetteer built around the Geonames.org dataset, that uses the Apache Lucene library to create a searchable gazetteer.
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","boost":0.5},{"location":"version-specific/supported-software/l/lDDT/","title":"lDDT","text":"The local Distance Difference Test (lDDT) is a superposition-free score which evaluates local distance differences in a model compared to a reference structure.
homepage: https://openstructure.org
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homepage: https://github.com/langchain-ai/langchain
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","boost":0.5},{"location":"version-specific/supported-software/l/langchain-openai/","title":"langchain-openai","text":"This package contains the LangChain integrations for OpenAI through their openai SDK.
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","boost":0.5},{"location":"version-specific/supported-software/l/lavaan/","title":"lavaan","text":"Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.
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","boost":0.5},{"location":"version-specific/supported-software/l/leafcutter/","title":"leafcutter","text":"Leafcutter quantifies RNA splicing variation using short-read RNA-seq data. The core idea is to leverage spliced reads (reads that span an intron) to quantify (differential) intron usage across samples. The advantages of this approach include: easy detection of novel introns, modeling of more complex splicing events than exonic PSI, avoiding the challenge of isoform abundance estimation, simple, computationally efficient algorithms scaling to 100s or even 1000s of samples. For details please see our bioRxiv preprint and corresponding Nature Genetics publication.
homepage: http://davidaknowles.github.io/leafcutter/index.html
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","boost":0.5},{"location":"version-specific/supported-software/l/leidenalg/","title":"leidenalg","text":"Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.
homepage: https://github.com/vtraag/leidenalg
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homepage: http://www.greenwoodsoftware.com/less/
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","boost":0.5},{"location":"version-specific/supported-software/l/lftp/","title":"lftp","text":"LFTP is a sophisticated ftp/http client, and a file transfer program supporting a number of network protocols. Like BASH, it has job control and uses the readline library for input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. It was designed with reliability in mind.
homepage: http://lftp.yar.ru
version toolchain 4.6.4 GNU/4.9.3-2.25 4.8.4 GCCcore/6.4.0 4.9.2 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libBigWig/","title":"libBigWig","text":"A C library for handling bigWig files
homepage: https://github.com/dpryan79/libBigWig
version toolchain 0.4.4 GCCcore/8.3.0 0.4.6 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libFLAME/","title":"libFLAME","text":"AMD fork of libFLAME. libFLAME is a portable library for dense matrix computations, providing much of the functionality present in LAPACK.
homepage: https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame
version versionsuffix toolchain 1.0 -amd GCC/7.3.0-2.30 2.2 -amd GCCcore/9.3.0 5.2.0 GCC/10.3.0 5.2.0 GCCcore/10.2.0 5.2.0 GCCcore/10.3.0 5.2.0 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libGDSII/","title":"libGDSII","text":"libGDSII is a C++ library for working with GDSII binary data files, intended primarily for use with the computational electromagnetism codes scuff-em and meep but sufficiently general-purpose to allow other uses as well.
homepage: https://github.com/HomerReid/libGDSII
version toolchain 0.21 GCCcore/10.2.0 0.21 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libGLU/","title":"libGLU","text":"The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.
homepage: https://mesa.freedesktop.org/archive/glu/
version versionsuffix toolchain 9.0.0 GCCcore/8.2.0 9.0.0 -Mesa-11.2.1 foss/2016a 9.0.0 foss/2016a 9.0.0 foss/2016b 9.0.0 foss/2017a 9.0.0 foss/2017b 9.0.0 foss/2018a 9.0.0 foss/2018b 9.0.0 fosscuda/2017b 9.0.0 fosscuda/2018a 9.0.0 fosscuda/2018b 9.0.0 gimkl/2.11.5 9.0.0 -Mesa-11.2.1 intel/2016a 9.0.0 intel/2016a 9.0.0 intel/2016b 9.0.0 intel/2017a 9.0.0 intel/2017b 9.0.0 intel/2018a 9.0.0 intel/2018b 9.0.0 intelcuda/2017b 9.0.0 iomkl/2018a 9.0.1 GCCcore/10.2.0 9.0.1 GCCcore/10.3.0 9.0.1 GCCcore/8.3.0 9.0.1 GCCcore/9.3.0 9.0.2 GCCcore/11.2.0 9.0.2 GCCcore/11.3.0 9.0.2 GCCcore/12.2.0 9.0.3 GCCcore/12.3.0 9.0.3 GCCcore/13.2.0 9.0.3 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libGridXC/","title":"libGridXC","text":"A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems. It is based on SiestaXC.
homepage: https://launchpad.net/libgridxc
version toolchain 0.8.5 iimpi/2019b 0.9.6 gompi/2020b 0.9.6 gompi/2021a 0.9.6 gompi/2021b 0.9.6 iimpi/2020b 0.9.6 iimpi/2021a 0.9.6 iimpi/2021b 1.1.0 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libICE/","title":"libICE","text":"X Inter-Client Exchange library for freedesktop.org
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.0.9 foss/2016a 1.0.9 gimkl/2.11.5 1.0.9 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libMemcached/","title":"libMemcached","text":"libMemcached is an open source C/C++ client library and tools for the memcached server (http://danga.com/memcached). It has been designed to be light on memory usage, thread safe, and provide full access to server side methods.
homepage: https://memcached.org
version toolchain 1.0.18 GCCcore/13.2.0 1.0.18 GCCcore/6.4.0 1.0.18 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libPSML/","title":"libPSML","text":"LibPSML provides a Fortran API to parse files in the PSeudopotential Markup Language (PSML) format.
homepage: https://launchpad.net/libpsml
version toolchain 1.1.10 GCC/10.2.0 1.1.10 GCC/10.3.0 1.1.10 GCC/11.2.0 1.1.10 iccifort/2020.4.304 1.1.10 intel-compilers/2021.2.0 1.1.10 intel-compilers/2021.4.0 1.1.12 GCC/11.3.0 1.1.7 foss/2016b 1.1.7 foss/2017a 1.1.8 iccifort/2019.5.281 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libQGLViewer/","title":"libQGLViewer","text":"libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers.
homepage: http://libqglviewer.com/
version versionsuffix toolchain 2.6.3 -Mesa-11.2.1 foss/2016a 2.6.3 foss/2016a 2.6.3 foss/2016b 2.6.3 -Mesa-11.2.1 intel/2016a 2.6.3 intel/2016b 2.6.4 intel/2016b 2.7.1 intel/2018a 2.8.0 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libRmath/","title":"libRmath","text":"The routines supporting the distribution and special functions in R and a few others are declared in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications.
homepage: https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library
version toolchain 3.6.0 foss/2018b 4.0.0 GCCcore/9.3.0 4.1.0 GCCcore/10.2.0 4.1.2 GCCcore/11.2.0 4.2.0 GCCcore/10.3.0 4.2.1 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libSBML/","title":"libSBML","text":"libSBML (Systems Biology Markup Language library) is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It's not an application itself (though it does come with example programs), but rather a library you embed in your own applications.
homepage: http://sbml.org/Software/libSBML
version toolchain 5.19.0 GCC/10.2.0 5.19.0 GCC/10.3.0 5.19.7 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libSM/","title":"libSM","text":"X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use.
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.2.2 foss/2016a 1.2.2 gimkl/2.11.5 1.2.2 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libStatGen/","title":"libStatGen","text":"Useful set of classes for creating statistical genetic programs.
homepage: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen
version toolchain 1.0.15 GCCcore/10.2.0 20190330 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libWallModelledLES/","title":"libWallModelledLES","text":"libWallModelledLES is a library based on OpenFOAM\u00ae technology, extending the capabilities of OpenFOAM in the area of wall-modelled LES (WMLES). This is a turbulence modelling methodology, which allows to make LES cheaper by not resolving the inner region of turbulent boundary layers.
homepage: https://bitbucket.org/lesituu/libwallmodelledles/
version toolchain 0.6.1 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libX11/","title":"libX11","text":"X11 client-side library
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.6.3 foss/2016a 1.6.3 gimkl/2.11.5 1.6.3 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXau/","title":"libXau","text":"The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display.
homepage: https://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.0.8 GCCcore/6.4.0 1.0.8 foss/2016a 1.0.8 gimkl/2.11.5 1.0.8 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXcursor/","title":"libXcursor","text":"X Cursor management library
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.1.14 foss/2016a 1.1.14 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXdamage/","title":"libXdamage","text":"X Damage extension library
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.1.4 foss/2016a 1.1.4 gimkl/2.11.5 1.1.4 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXdmcp/","title":"libXdmcp","text":"The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager.
homepage: https://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.1.2 GCCcore/6.4.0 1.1.2 foss/2016a 1.1.2 gimkl/2.11.5 1.1.2 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXext/","title":"libXext","text":"Common X Extensions library
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.3.3 foss/2016a 1.3.3 gimkl/2.11.5 1.3.3 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXfixes/","title":"libXfixes","text":"X Fixes extension library
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 5.0.1 foss/2016a 5.0.1 gimkl/2.11.5 5.0.1 intel/2016a 5.0.2 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXfont/","title":"libXfont","text":"X font libary
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version versionsuffix toolchain 1.5.1 -freetype-2.6.3 foss/2016a 1.5.1 foss/2016a 1.5.1 gimkl/2.11.5 1.5.1 -freetype-2.6.3 intel/2016a 1.5.1 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXft/","title":"libXft","text":"X11 client-side library
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version versionsuffix toolchain 2.3.2 -freetype-2.6.3 foss/2016a 2.3.2 foss/2016a 2.3.2 -fontconfig-2.11.95 intel/2016a 2.3.2 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXi/","title":"libXi","text":"LibXi provides an X Window System client interface to the XINPUT extension to the X protocol.
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.7.6 foss/2016a 1.7.6 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXinerama/","title":"libXinerama","text":"Xinerama multiple monitor library
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.1.3 foss/2016a 1.1.3 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXmu/","title":"libXmu","text":"libXmu provides a set of miscellaneous utility convenience functions for X libraries to use. libXmuu is a lighter-weight version that does not depend on libXt or libXext
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.1.2 foss/2016a 1.1.2 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXp/","title":"libXp","text":"libXp provides the X print library.
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.0.3 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXpm/","title":"libXpm","text":"libXp provides the X print library.
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 3.5.11 foss/2016a 3.5.11 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXrandr/","title":"libXrandr","text":"X Resize, Rotate and Reflection extension library
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.5.0 foss/2016a 1.5.0 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXrender/","title":"libXrender","text":"X11 client-side library
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 0.9.9 foss/2016a 0.9.9 gimkl/2.11.5 0.9.9 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXt/","title":"libXt","text":"libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.1.5 foss/2016a 1.1.5 gimkl/2.11.5 1.1.5 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libXxf86vm/","title":"libXxf86vm","text":"X11 XFree86 video mode extension library
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.1.4 foss/2016a 1.1.4 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libabigail/","title":"libabigail","text":"ABIGAIL stands for the Application Binary Interface Generic Analysis and Instrumentation Library. It\u2019s a framework which aims at helping developers and software distributors to spot some ABI-related issues like interface incompatibility in ELF shared libraries by performing a static analysis of the ELF binaries at hand. The type of interface incompatibilities that Abigail focuses on is related to changes on the exported ELF functions and variables symbols, as well as layout and size changes of data types of the functions and variables exported by shared libraries. In other words, if the return type of a function exported by a shared library changes in an incompatible way from one version of a given shared library to another, we want Abigail to help people catch that.
homepage: https://sourceware.org/libabigail
version toolchain 2.5 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libaec/","title":"libaec","text":"Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). The library achieves best results for low entropy data as often encountered in space imaging instrument data or numerical model output from weather or climate simulations. While floating point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.
homepage: https://gitlab.dkrz.de/k202009/libaec
version toolchain 1.0.6 GCCcore/10.2.0 1.0.6 GCCcore/10.3.0 1.0.6 GCCcore/11.2.0 1.0.6 GCCcore/11.3.0 1.0.6 GCCcore/12.2.0 1.0.6 GCCcore/12.3.0 1.0.6 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libaed2/","title":"libaed2","text":"libaed2 is a library of modules and algorithms for simulation of \"aquatic ecodynamics\" - water quality, aquatic biogeochemsitry, biotic habitat and aquatic ecosystem dynamics.
homepage: https://aquatic.science.uwa.edu.au/research/models/AED
version toolchain 1.3.0 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libaio/","title":"libaio","text":"Asynchronous input/output library that uses the kernels native interface.
homepage: https://pagure.io/libaio
version toolchain 0.3.111 GCCcore/8.2.0 0.3.111 GCCcore/8.3.0 0.3.112 GCCcore/10.2.0 0.3.112 GCCcore/10.3.0 0.3.112 GCCcore/11.2.0 0.3.112 GCCcore/11.3.0 0.3.113 GCCcore/12.2.0 0.3.113 GCCcore/12.3.0 0.3.113 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libarchive/","title":"libarchive","text":"Multi-format archive and compression library
homepage: https://www.libarchive.org/
version toolchain 3.4.0 GCCcore/8.2.0 3.4.2 GCCcore/9.3.0 3.4.3 GCCcore/10.2.0 3.5.1 GCCcore/10.3.0 3.5.1 GCCcore/11.2.0 3.5.1 GCCcore/8.3.0 3.6.1 GCCcore/11.3.0 3.6.1 GCCcore/12.2.0 3.6.2 GCCcore/12.3.0 3.6.2 GCCcore/13.1.0 3.7.2 GCCcore/13.2.0 3.7.4 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libav/","title":"libav","text":"Libav is a friendly and community-driven effort to provide its users with a set of portable, functional and high-performance libraries for dealing with multimedia formats of all sorts.
homepage: https://libav.org/
version toolchain 11.10 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libavif/","title":"libavif","text":"This library aims to be a friendly, portable C implementation of the AV1 Image File Format, as described here: https://aomediacodec.github.io/av1-avif/
homepage: https://github.com/AOMediaCodec/libavif
version toolchain 0.11.1 GCCcore/10.3.0 0.11.1 GCCcore/11.3.0 0.9.0 foss/2020b 1.0.4 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 2.1.1 foss/2016a 2.1.1 intel/2016a 2.2.3 foss/2016b 2.2.3 intel/2016b 2.2.4 GCCcore/6.4.0 2.2.4 foss/2016b 2.2.4 intel/2017a 2.2.5 GCCcore/6.4.0 2.2.5 GCCcore/7.3.0 2.2.5 GCCcore/8.2.0 2.2.5 GCCcore/8.3.0 2.2.5 intel/2017b 2.2.5 intel/2018a 2.3.0 GCCcore/10.2.0 2.3.0 GCCcore/9.3.0 2.3.1 GCCcore/10.3.0 2.3.3 GCCcore/11.2.0 2.3.3 GCCcore/11.3.0 2.3.3 GCCcore/12.2.0 2.3.3 GCCcore/12.3.0 2.3.3 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libgdiplus/","title":"libgdiplus","text":"Libgdiplus is the Mono library that provides a GDI+-compatible API on non-Windows operating systems.
homepage: https://www.mono-project.com/docs/gui/libgdiplus
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","boost":0.5},{"location":"version-specific/supported-software/l/libgeotiff/","title":"libgeotiff","text":"Library for reading and writing coordinate system information from/to GeoTIFF files
homepage: https://directory.fsf.org/wiki/Libgeotiff
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","boost":0.5},{"location":"version-specific/supported-software/l/libgit2/","title":"libgit2","text":"libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings.
homepage: https://libgit2.org/
version toolchain 1.0.0 GCCcore/8.3.0 1.1.0 GCCcore/10.2.0 1.1.0 GCCcore/10.3.0 1.1.0 GCCcore/9.3.0 1.1.1 GCCcore/11.2.0 1.4.3 GCCcore/11.3.0 1.5.0 GCCcore/12.2.0 1.7.1 GCCcore/12.3.0 1.7.2 GCCcore/13.2.0 1.8.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libglade/","title":"libglade","text":"Libglade is a library for constructing user interfaces dynamically from XML descriptions.
homepage: https://developer.gnome.org/libglade/
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","boost":0.5},{"location":"version-specific/supported-software/l/libglvnd/","title":"libglvnd","text":"libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.
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","boost":0.5},{"location":"version-specific/supported-software/l/libgpg-error/","title":"libgpg-error","text":"Libgpg-error is a small library that defines common error values for all GnuPG components.
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","boost":0.5},{"location":"version-specific/supported-software/l/libgpuarray/","title":"libgpuarray","text":"Library to manipulate tensors on the GPU.
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","boost":0.5},{"location":"version-specific/supported-software/l/libgtextutils/","title":"libgtextutils","text":"ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream
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version toolchain 0.7 GCCcore/7.3.0 0.7 foss/2016a 0.7 foss/2016b 0.7 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libgxps/","title":"libgxps","text":"libgxps is a GObject based library for handling and rendering XPS documents.
homepage: https://wiki.gnome.org/Projects/libgxps
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","boost":0.5},{"location":"version-specific/supported-software/l/libhandy/","title":"libhandy","text":"Building blocks for modern adaptive GNOME apps
homepage: https://gnome.pages.gitlab.gnome.org/libhandy/
version toolchain 1.8.2 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libharu/","title":"libharu","text":"libHaru is a free, cross platform, open source library for generating PDF files.
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","boost":0.5},{"location":"version-specific/supported-software/l/libheif/","title":"libheif","text":"libheif is an HEIF and AVIF file format decoder and encoder
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","boost":0.5},{"location":"version-specific/supported-software/l/libhomfly/","title":"libhomfly","text":"This is basically a conversion of the program written by Robert J Jenkins Jr into a shared library. It accepts as entry a character string, formatted in the same way as the input files that the original code used (see below). The returned value is the string that the original program would print on screen.
homepage: https://github.com/miguelmarco/libhomfly
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","boost":0.5},{"location":"version-specific/supported-software/l/libibmad/","title":"libibmad","text":"libibmad is a convenience library to encode, decode, and dump IB MAD packets. It is implemented on top of and in conjunction with libibumad (the umad kernel interface library.)
homepage: http://www.openfabrics.org
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","boost":0.5},{"location":"version-specific/supported-software/l/libibumad/","title":"libibumad","text":"libibumad is the umad kernel interface library.
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","boost":0.5},{"location":"version-specific/supported-software/l/libiconv/","title":"libiconv","text":"Libiconv converts from one character encoding to another through Unicode conversion
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homepage: http://www.gnu.org/software/libidn
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","boost":0.5},{"location":"version-specific/supported-software/l/libidn2/","title":"libidn2","text":"GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn's purpose is to encode and decode internationalized domain names.
homepage: https://www.gnu.org/software/libidn
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","boost":0.5},{"location":"version-specific/supported-software/l/libjpeg-turbo/","title":"libjpeg-turbo","text":"libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.
homepage: http://sourceforge.net/projects/libjpeg-turbo/
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","boost":0.5},{"location":"version-specific/supported-software/l/libjxl/","title":"libjxl","text":"JPEG XL image format reference implementation
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","boost":0.5},{"location":"version-specific/supported-software/l/libleidenalg/","title":"libleidenalg","text":"Implements the Leiden algorithm in C++
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","boost":0.5},{"location":"version-specific/supported-software/l/libmad/","title":"libmad","text":"MAD is a high-quality MPEG audio decoder.
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","boost":0.5},{"location":"version-specific/supported-software/l/libmbd/","title":"libmbd","text":"Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd.
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","boost":0.5},{"location":"version-specific/supported-software/l/libmo_unpack/","title":"libmo_unpack","text":"A library for handling the WGDOS and RLE compression schemes used in UM files.
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","boost":0.5},{"location":"version-specific/supported-software/l/libnsl/","title":"libnsl","text":"The libnsl package contains the public client interface for NIS(YP).
homepage: https://github.com/thkukuk/libnsl
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","boost":0.5},{"location":"version-specific/supported-software/l/libobjcryst/","title":"libobjcryst","text":"ObjCryst++ is Object-Oriented Crystallographic Library for C++
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","boost":0.5},{"location":"version-specific/supported-software/l/libogg/","title":"libogg","text":"Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.
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","boost":0.5},{"location":"version-specific/supported-software/l/libosmium/","title":"libosmium","text":"A fast and flexible C++ library for working with OpenStreetMap data. The Osmium Library has extensive support for all types of OSM entities: nodes, ways, relations, and changesets. It allows reading from and writing to OSM files in XML and PBF formats, including change files and full history files. Osmium can store OSM data in memory and on disk in various formats and using various indexes. Its easy to use handler interface allows you to quickly write data filtering and conversion functions. Osmium can create WKT, WKB, OGR, GEOS and GeoJSON geometries for easy conversion into many GIS formats and it can assemble multipolygons from ways and relations.
homepage: https://osmcode.org/libosmium/
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","boost":0.5},{"location":"version-specific/supported-software/l/libpci/","title":"libpci","text":"Library for portable access to PCI bus configuration registers from PCI Utils.
homepage: https://github.com/pciutils/pciutils
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","boost":0.5},{"location":"version-specific/supported-software/l/libpciaccess/","title":"libpciaccess","text":"Generic PCI access library.
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version toolchain 0.13.4 foss/2016a 0.13.4 foss/2016b 0.13.4 gimkl/2.11.5 0.13.4 intel/2016a 0.13.4 intel/2016b 0.14 GCCcore/6.4.0 0.14 GCCcore/7.2.0 0.14 GCCcore/7.3.0 0.14 GCCcore/8.2.0 0.14 GCCcore/8.3.0 0.16 GCCcore/10.2.0 0.16 GCCcore/10.3.0 0.16 GCCcore/11.2.0 0.16 GCCcore/11.3.0 0.16 GCCcore/9.2.0 0.16 GCCcore/9.3.0 0.17 GCCcore/12.2.0 0.17 GCCcore/12.3.0 0.17 GCCcore/13.2.0 0.18.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libplinkio/","title":"libplinkio","text":"A small C and Python library for reading PLINK genotype files.
homepage: https://github.com/mfranberg/libplinkio
version toolchain 0.9.8 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libpng/","title":"libpng","text":"libpng is the official PNG reference library
homepage: http://www.libpng.org/pub/png/libpng.html
version toolchain 1.2.58 system 1.2.59 system 1.5.30 system 1.6.21 foss/2016a 1.6.21 gimkl/2.11.5 1.6.21 intel/2016a 1.6.23 foss/2016a 1.6.23 foss/2016b 1.6.23 intel/2016b 1.6.24 GCCcore/4.9.3 1.6.24 GCCcore/5.4.0 1.6.24 foss/2016b 1.6.24 intel/2016b 1.6.26 foss/2016b 1.6.26 intel/2016b 1.6.27 intel/2016b 1.6.28 GCCcore/5.4.0 1.6.28 GCCcore/6.3.0 1.6.28 gimkl/2017a 1.6.29 GCCcore/6.3.0 1.6.32 GCCcore/6.4.0 1.6.34 GCCcore/6.4.0 1.6.34 GCCcore/7.3.0 1.6.36 GCCcore/8.2.0 1.6.37 GCCcore/10.2.0 1.6.37 GCCcore/10.3.0 1.6.37 GCCcore/11.2.0 1.6.37 GCCcore/11.3.0 1.6.37 GCCcore/8.3.0 1.6.37 GCCcore/9.3.0 1.6.38 GCCcore/12.2.0 1.6.39 GCCcore/12.3.0 1.6.40 GCCcore/13.2.0 1.6.43 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libpsl/","title":"libpsl","text":"C library for the Public Suffix List
homepage: https://rockdaboot.github.io/libpsl
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","boost":0.5},{"location":"version-specific/supported-software/l/libpsortb/","title":"libpsortb","text":"PSORT family of programs for subcellular localization prediction as well as other datasets and resources relevant to localization prediction.
homepage: http://psort.org/
version toolchain 1.0 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libpspio/","title":"libpspio","text":"libpspio is a library to read and write pseudopotentials in multiple formats.
homepage: https://gitlab.e-cam2020.eu/esl/pspio/
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","boost":0.5},{"location":"version-specific/supported-software/l/libpthread-stubs/","title":"libpthread-stubs","text":"The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
homepage: http://xcb.freedesktop.org/
version toolchain 0.3 GCCcore/6.4.0 0.3 foss/2016a 0.3 foss/2016b 0.3 gimkl/2.11.5 0.3 intel/2016a 0.3 intel/2016b 0.4 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libreadline/","title":"libreadline","text":"The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
homepage: http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html
version toolchain 6.3 GCC/4.8.2 6.3 GCC/4.8.4 6.3 GCC/4.9.2 6.3 GCC/4.9.3-2.25 6.3 GCC/5.4.0-2.26 6.3 GCCcore/4.9.3 6.3 GCCcore/5.4.0 6.3 GCCcore/6.3.0 6.3 GNU/4.9.3-2.25 6.3 foss/2016.04 6.3 foss/2016a 6.3 foss/2016b 6.3 gimkl/2.11.5 6.3 gimkl/2017a 6.3 intel/2016.02-GCC-4.9 6.3 intel/2016a 6.3 intel/2016b 6.3 iomkl/2016.07 6.3 iomkl/2016.09-GCC-4.9.3-2.25 6.3 system 7.0 GCCcore/6.3.0 7.0 GCCcore/6.4.0 7.0 GCCcore/7.2.0 7.0 GCCcore/7.3.0 8.0 GCCcore/10.2.0 8.0 GCCcore/8.2.0 8.0 GCCcore/8.3.0 8.0 GCCcore/9.3.0 8.0 system 8.1 GCCcore/10.3.0 8.1 GCCcore/11.2.0 8.1 GCCcore/11.3.0 8.1.2 GCCcore/11.3.0 8.1.2 GCCcore/12.1.0 8.2 GCCcore/12.2.0 8.2 GCCcore/12.3.0 8.2 GCCcore/13.1.0 8.2 GCCcore/13.2.0 8.2 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/librosa/","title":"librosa","text":"Audio and music processing in Python
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","boost":0.5},{"location":"version-specific/supported-software/l/librsb/","title":"librsb","text":"A shared memory parallel sparse matrix computations library for the Recursive Sparse Blocks format
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","boost":0.5},{"location":"version-specific/supported-software/l/librsvg/","title":"librsvg","text":"librsvg is a library to render SVG files using cairo.
homepage: https://wiki.gnome.org/action/show/Projects/LibRsvg
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","boost":0.5},{"location":"version-specific/supported-software/l/librttopo/","title":"librttopo","text":"The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies using user-provided data stores.
homepage: https://git.osgeo.org/gitea/rttopo/librttopo
version toolchain 1.1.0 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libsamplerate/","title":"libsamplerate","text":"Secret Rabbit Code (aka libsamplerate) is a Sample Rate Converter for audio.
homepage: http://www.mega-nerd.com/libsamplerate
version toolchain 0.1.9 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libsigc%2B%2B/","title":"libsigc++","text":"The libsigc++ package implements a typesafe callback system for standard C++.
homepage: http://www.gtk.org/
version toolchain 2.10.0 GCCcore/6.4.0 2.10.1 GCCcore/7.3.0 2.10.2 GCCcore/8.2.0 2.10.2 GCCcore/8.3.0 2.10.8 GCCcore/10.3.0 2.12.1 GCCcore/11.3.0 3.4.0 GCCcore/11.3.0 3.6.0 GCCcore/12.2.0 3.6.0 GCCcore/12.3.0 3.6.0 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libsigsegv/","title":"libsigsegv","text":"GNU libsigsegv is a library for handling page faults in user mode.
homepage: https://www.gnu.org/software/libsigsegv/
version toolchain 2.11 GCCcore/6.4.0 2.12 GCCcore/9.3.0 2.13 GCCcore/10.2.0 2.14 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libsndfile/","title":"libsndfile","text":"Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.
homepage: http://www.mega-nerd.com/libsndfile
version toolchain 1.0.28 GCCcore/10.2.0 1.0.28 GCCcore/6.4.0 1.0.28 GCCcore/7.3.0 1.0.28 GCCcore/8.2.0 1.0.28 GCCcore/8.3.0 1.0.28 GCCcore/9.3.0 1.0.28 intel/2017a 1.0.31 GCCcore/10.3.0 1.0.31 GCCcore/11.2.0 1.1.0 GCCcore/11.3.0 1.2.0 GCCcore/12.2.0 1.2.2 GCCcore/12.3.0 1.2.2 GCCcore/13.2.0 1.2.2 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libsodium/","title":"libsodium","text":"Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.
homepage: https://doc.libsodium.org/
version toolchain 1.0.11 foss/2016b 1.0.11 intel/2016b 1.0.12 GCCcore/6.4.0 1.0.12 intel/2017a 1.0.13 GCCcore/6.4.0 1.0.13 foss/2017a 1.0.16 GCCcore/6.4.0 1.0.16 GCCcore/7.3.0 1.0.17 GCCcore/8.2.0 1.0.18 GCCcore/10.2.0 1.0.18 GCCcore/10.3.0 1.0.18 GCCcore/11.2.0 1.0.18 GCCcore/11.3.0 1.0.18 GCCcore/12.2.0 1.0.18 GCCcore/12.3.0 1.0.18 GCCcore/8.3.0 1.0.18 GCCcore/9.3.0 1.0.19 GCCcore/13.2.0 1.0.20 GCCcore/13.3.0 1.0.6 intel/2016a 1.0.8 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libspatialindex/","title":"libspatialindex","text":"C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API
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","boost":0.5},{"location":"version-specific/supported-software/l/libspatialite/","title":"libspatialite","text":"SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.
homepage: https://www.gaia-gis.it/fossil/libspatialite/home
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","boost":0.5},{"location":"version-specific/supported-software/l/libspectre/","title":"libspectre","text":"libspectre is a small library for rendering Postscript documents. It provides a convenient easy to use API for handling and rendering Postscript documents.
homepage: https://www.freedesktop.org/wiki/Software/libspectre/
version toolchain 0.2.12 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libssh/","title":"libssh","text":"Multiplatform C library implementing the SSHv2 protocol on client and server side
homepage: https://www.libssh.org
version toolchain 0.9.0 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libsupermesh/","title":"libsupermesh","text":"libsupermesh parallel supermeshing library.
homepage: https://github.com/firedrakeproject/libsupermesh
version toolchain 2025-01-25 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libtar/","title":"libtar","text":"C library for manipulating POSIX tar files
homepage: https://repo.or.cz/libtar.git
version toolchain 1.2.20 GCCcore/7.3.0 1.2.20 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libtasn1/","title":"libtasn1","text":"Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. It was written by Fabio Fiorina, and has been shipped as part of GnuTLS for some time but is now a proper GNU package.
homepage: https://www.gnu.org/software/libtasn1/
version toolchain 4.12 GCCcore/5.4.0 4.13 GCCcore/7.3.0 4.13 GCCcore/8.2.0 4.16.0 GCCcore/10.2.0 4.16.0 GCCcore/8.3.0 4.17.0 GCCcore/10.3.0 4.18.0 GCCcore/11.2.0 4.19.0 GCCcore/11.3.0 4.19.0 GCCcore/12.3.0 4.7 GNU/4.9.3-2.25 4.7 foss/2016a 4.7 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libtecla/","title":"libtecla","text":"The tecla library provides UNIX and LINUX programs with interactive command line editing facilities, similar to those of the UNIX tcsh shell. In addition to simple command-line editing, it supports recall of previously entered command lines, TAB completion of file names or other tokens, and in-line wild-card expansion of filenames. The internal functions which perform file-name completion and wild-card expansion are also available externally for optional use by programs.
homepage: https://sites.astro.caltech.edu/~mcs/tecla/
version toolchain 1.6.3 GCCcore/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libtirpc/","title":"libtirpc","text":"Libtirpc is a port of Suns Transport-Independent RPC library to Linux.
homepage: https://sourceforge.net/projects/libtirpc/
version toolchain 1.1.4 GCCcore/7.3.0 1.1.4 GCCcore/8.2.0 1.2.6 GCCcore/8.3.0 1.2.6 GCCcore/9.3.0 1.3.1 GCCcore/10.2.0 1.3.2 GCCcore/10.3.0 1.3.2 GCCcore/11.2.0 1.3.2 GCCcore/11.3.0 1.3.3 GCCcore/12.2.0 1.3.3 GCCcore/12.3.0 1.3.4 GCCcore/13.2.0 1.3.5 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libtool/","title":"libtool","text":"GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
homepage: http://www.gnu.org/software/libtool
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","boost":0.5},{"location":"version-specific/supported-software/l/libunistring/","title":"libunistring","text":"This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
homepage: https://www.gnu.org/software/libunistring/
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","boost":0.5},{"location":"version-specific/supported-software/l/libunwind/","title":"libunwind","text":"The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications
homepage: http://www.nongnu.org/libunwind/
version toolchain 1.1 GCC/4.9.2 1.1 foss/2016a 1.1 intel/2016b 1.2.1 GCCcore/6.3.0 1.2.1 GCCcore/6.4.0 1.2.1 GCCcore/7.3.0 1.2.1 foss/2016b 1.3.1 GCCcore/8.2.0 1.3.1 GCCcore/8.3.0 1.3.1 GCCcore/9.3.0 1.4.0 GCCcore/10.2.0 1.4.0 GCCcore/10.3.0 1.5.0 GCCcore/10.3.0 1.5.0 GCCcore/11.2.0 1.6.2 GCCcore/11.3.0 1.6.2 GCCcore/12.2.0 1.6.2 GCCcore/12.3.0 1.6.2 GCCcore/13.2.0 1.8.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libutempter/","title":"libutempter","text":"libutempter is library that provides an interface for terminal emulators such as screen and xterm to record user sessions to utmp and wtmp files.
homepage: http://git.altlinux.org/people/ldv/packages/?p=libutempter.git
version toolchain 1.1.6.2 GCC/6.4.0-2.28 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libuv/","title":"libuv","text":"libuv is a multi-platform support library with a focus on asynchronous I/O.
homepage: https://libuv.org
version toolchain 1.37.0 GCCcore/8.3.0 1.48.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libvdwxc/","title":"libvdwxc","text":"libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.
homepage: https://libvdwxc.materialsmodeling.org/
version toolchain 0.3.2 foss/2018b 0.4.0 foss/2019a 0.4.0 foss/2019b 0.4.0 foss/2020a 0.4.0 foss/2020b 0.4.0 foss/2021a 0.4.0 foss/2021b 0.4.0 foss/2022a 0.4.0 foss/2023a 0.4.0 intel/2020b 0.4.0 intel/2021a 0.4.0 intel/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libvorbis/","title":"libvorbis","text":"Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format
homepage: https://xiph.org/vorbis/
version toolchain 1.3.7 GCCcore/10.2.0 1.3.7 GCCcore/10.3.0 1.3.7 GCCcore/11.2.0 1.3.7 GCCcore/11.3.0 1.3.7 GCCcore/12.2.0 1.3.7 GCCcore/12.3.0 1.3.7 GCCcore/13.2.0 1.3.7 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libvori/","title":"libvori","text":"C++ library implementing the Voronoi integration as well as the compressed bqb file format. The present version of libvori is a very early development version, which is hard-coded to work with the CP2k program package.
homepage: https://brehm-research.de/libvori.php
version toolchain 220621 GCCcore/11.3.0 220621 GCCcore/12.2.0 220621 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libwebp/","title":"libwebp","text":"WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster.
homepage: https://developers.google.com/speed/webp
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","boost":0.5},{"location":"version-specific/supported-software/l/libwpe/","title":"libwpe","text":"WPE is the reference WebKit port for embedded and low-consumption computer devices. It has been designed from the ground-up with performance, small footprint, accelerated content rendering, and simplicity of deployment in mind, bringing the excellence of the WebKit engine to countless platforms and target devices.
homepage: https://webkit.org/wpe
version toolchain 1.13.3 GCCcore/11.2.0 1.14.1 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libxc/","title":"libxc","text":"Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.
homepage: https://www.tddft.org/programs/libxc
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","boost":0.5},{"location":"version-specific/supported-software/l/libxcb/","title":"libxcb","text":"The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
homepage: http://xcb.freedesktop.org/
version toolchain 1.11.1 foss/2016a 1.11.1 gimkl/2.11.5 1.11.1 intel/2016a 1.13 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libxkbcommon/","title":"libxkbcommon","text":"xkbcommon is a library to handle keyboard descriptions, including loading them from disk, parsing them and handling their state. It's mainly meant for client toolkits, window systems, and other system applications.
homepage: http://xkbcommon.org/
version toolchain 0.6.1 foss/2016a 0.6.1 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libxml%2B%2B/","title":"libxml++","text":"libxml++ is a C++ wrapper for the libxml XML parser library.
homepage: http://libxmlplusplus.sourceforge.net
version toolchain 2.40.1 GCCcore/7.3.0 2.40.1 GCCcore/8.2.0 2.40.1 GCCcore/8.3.0 2.42.1 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libxml2-python/","title":"libxml2-python","text":"Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). This is the Python binding.
homepage: http://xmlsoft.org/
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","boost":0.5},{"location":"version-specific/supported-software/l/libxml2/","title":"libxml2","text":"Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
homepage: http://xmlsoft.org/
version versionsuffix toolchain 2.10.3 GCCcore/12.2.0 2.11.4 GCCcore/12.3.0 2.11.5 GCCcore/13.2.0 2.12.7 GCCcore/13.3.0 2.9.10 GCCcore/10.2.0 2.9.10 GCCcore/10.3.0 2.9.10 GCCcore/11.2.0 2.9.10 GCCcore/9.2.0 2.9.10 GCCcore/9.3.0 2.9.13 GCCcore/11.3.0 2.9.2 GCC/4.8.3 2.9.2 GCC/4.8.4 2.9.2 GCC/4.9.2 2.9.2 GCC/4.9.3-2.25 2.9.2 GNU/4.9.3-2.25 2.9.3 GCC/4.9.3-2.25 2.9.3 -Python-2.7.11 foss/2016a 2.9.3 foss/2016a 2.9.3 gimkl/2.11.5 2.9.3 -Python-2.7.11 intel/2016a 2.9.3 intel/2016a 2.9.4 GCC/5.4.0-2.26 2.9.4 GCCcore/4.9.3 2.9.4 GCCcore/5.4.0 2.9.4 GCCcore/6.3.0 2.9.4 GCCcore/6.4.0 2.9.4 foss/2016.04 2.9.4 foss/2016a 2.9.4 -Python-2.7.12 foss/2016b 2.9.4 foss/2016b 2.9.4 gimkl/2017a 2.9.4 -Python-2.7.12 intel/2016b 2.9.4 intel/2016b 2.9.4 -Python-2.7.13 intel/2017a 2.9.5 GCCcore/6.3.0 2.9.6 GCCcore/6.4.0 2.9.7 GCCcore/6.4.0 2.9.8 GCCcore/6.4.0 2.9.8 GCCcore/7.2.0 2.9.8 GCCcore/7.3.0 2.9.8 GCCcore/8.2.0 2.9.9 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libxslt/","title":"libxslt","text":"Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
homepage: http://xmlsoft.org/
version versionsuffix toolchain 1.1.28 foss/2016a 1.1.28 -Python-2.7.11 intel/2016a 1.1.28 intel/2016a 1.1.29 foss/2016b 1.1.29 intel/2016a 1.1.29 intel/2016b 1.1.29 intel/2017a 1.1.30 GCCcore/6.3.0 1.1.32 GCCcore/6.4.0 1.1.32 GCCcore/7.3.0 1.1.33 GCCcore/8.2.0 1.1.34 GCCcore/10.2.0 1.1.34 GCCcore/10.3.0 1.1.34 GCCcore/11.2.0 1.1.34 GCCcore/11.3.0 1.1.34 GCCcore/8.3.0 1.1.34 GCCcore/9.3.0 1.1.37 GCCcore/12.2.0 1.1.38 GCCcore/12.3.0 1.1.38 GCCcore/13.2.0 1.1.42 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/libxsmm/","title":"libxsmm","text":"LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).
homepage: https://github.com/hfp/libxsmm
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","boost":0.5},{"location":"version-specific/supported-software/l/libyaml/","title":"libyaml","text":"LibYAML is a YAML parser and emitter written in C.
homepage: http://pyyaml.org/wiki/LibYAML
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","boost":0.5},{"location":"version-specific/supported-software/l/libzeep/","title":"libzeep","text":"Libzeep was originally developed to make it easy to create SOAP servers.
homepage: https://github.com/mhekkel/libzeep
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","boost":0.5},{"location":"version-specific/supported-software/l/libzip/","title":"libzip","text":"libzip is a C library for reading, creating, and modifying zip archives.
homepage: https://libzip.org/
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","boost":0.5},{"location":"version-specific/supported-software/l/lie_learn/","title":"lie_learn","text":"lie_learn is a python package that knows how to do various tricky computations related to Lie groups and manifolds (mainly the sphere S2 and rotation group SO3).
homepage: https://github.com/AMLab-Amsterdam/lie_learn
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","boost":0.5},{"location":"version-specific/supported-software/l/lifelines/","title":"lifelines","text":"lifelines is a pure Python implementation of the best parts of survival analysis
homepage: https://lifelines.readthedocs.io
version versionsuffix toolchain 0.22.8 -Python-3.7.2 fosscuda/2019a 0.26.3 fosscuda/2020b 0.27.4 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/liknorm/","title":"liknorm","text":"Moments of the product of an exponential-family likelihood with a Normal distribution.
homepage: https://github.com/limix/liknorm
version toolchain 1.5.2 GCCcore/7.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/likwid/","title":"likwid","text":"Likwid stands for Like I knew what I am doing. This project contributes easy to use command line tools for Linux to support programmers in developing high performance multi threaded programs.
homepage: http://code.google.com/p/likwid/
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","boost":0.5},{"location":"version-specific/supported-software/l/lil-aretomo/","title":"lil-aretomo","text":"A lightweight Python API for AreTomo.
homepage: https://github.com/teamtomo/lil-aretomo
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","boost":0.5},{"location":"version-specific/supported-software/l/limix/","title":"limix","text":"Limix is a flexible and efficient linear mixed model library with interfaces to Python. Genomic analyses require flexible models that can be adapted to the needs of the user. Limix is smart about how particular models are fitted to save computational cost.
homepage: https://github.com/limix/limix
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","boost":0.5},{"location":"version-specific/supported-software/l/line_profiler/","title":"line_profiler","text":"line_profiler is a module for doing line-by-line profiling of functions. kernprof is a convenient script for running either line_profiler or the Python standard library's cProfile or profile modules, depending on what is available.
homepage: https://github.com/pyutils/line_profiler
version versionsuffix toolchain 3.1.0 -Python-3.8.2 foss/2020a 3.5.1 foss/2021b 4.0.0 foss/2022a 4.1.1 GCCcore/12.2.0 4.1.2 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://llvm.org/docs/CommandGuide/lit.html
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homepage: https://github.com/OpenHydrology/lmoments3
version toolchain 1.0.6 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/logaddexp/","title":"logaddexp","text":"C library that implements the logarithm of the sum of exponentiations. Inspired by NumPy's logaddexp function.
homepage: https://github.com/horta/logaddexp
version toolchain 1.0.3 GCCcore/7.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/longestrunsubsequence/","title":"longestrunsubsequence","text":"Implementation of a solver for the Longest Run Subsequence Problem. Given a sequence as input, compute a longest subsequence such that there is at most one run for every character.
homepage: https://pypi.org/project/longestrunsubsequence/
version toolchain 1.0.1 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/longread_umi/","title":"longread_umi","text":"A collection of scripts for processing longread UMI data.
homepage: https://github.com/SorenKarst/longread_umi
version toolchain 0.3.2 foss/2020b 0.3.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/loomR/","title":"loomR","text":"An R interface for loom files
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version versionsuffix toolchain 0.2.0-20180425 -R-4.2.1 foss/2022a 0.2.0-20180425 -R-4.2.2 foss/2022b 0.2.0-20180425 -R-4.3.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/loompy/","title":"loompy","text":"Python implementation of the Loom file format, an efficient file format for large omics datasets
homepage: https://loompy.org/
version toolchain 3.0.6 intel/2020b 3.0.7 foss/2021a 3.0.7 foss/2021b 3.0.7 foss/2022a 3.0.7 foss/2023a 3.0.7 intel/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/lpsolve/","title":"lpsolve","text":"Mixed Integer Linear Programming (MILP) solver
homepage: https://sourceforge.net/projects/lpsolve/
version toolchain 5.5.2.11 GCC/10.2.0 5.5.2.11 GCC/10.3.0 5.5.2.11 GCC/11.2.0 5.5.2.11 GCC/11.3.0 5.5.2.11 GCC/12.2.0 5.5.2.11 GCC/9.3.0 5.5.2.5 GCC/6.4.0-2.28 5.5.2.5 GCC/8.3.0 5.5.2.5 foss/2018a 5.5.2.5 iccifort/2017.4.196-GCC-6.4.0-2.28 5.5.2.5 iccifort/2019.1.144-GCC-8.2.0-2.31.1 5.5.2.5 iccifort/2019.5.281 5.5.2.5 intel/2017a 5.5.2.5 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/lrcalc/","title":"lrcalc","text":"The Littlewood-Richardson Calculator is a program designed to compute Littlewood-Richardson coefficients.
homepage: https://sites.math.rutgers.edu/~asbuch/lrcalc/
version toolchain 2.1 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/lrslib/","title":"lrslib","text":"lrslib is a self-contained ANSI C implementation of the reverse search algorithm for vertex enumeration/convex hull problems
homepage: http://cgm.cs.mcgill.ca/~avis/C/lrs.html
version toolchain 6.2 intel/2018b 7.0a gompi/2019a 7.2 gompi/2022a 7.2 gompi/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/lwgrp/","title":"lwgrp","text":"The Light-weight Group Library provides methods for MPI codes to quickly create and destroy process groups
homepage: https://github.com/llnl/lwgrp
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","boost":0.5},{"location":"version-specific/supported-software/l/lxml/","title":"lxml","text":"The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.
homepage: http://lxml.de/
version versionsuffix toolchain 3.5.0 -Python-2.7.11 intel/2016a 3.6.0 -Python-2.7.11 intel/2016a 3.6.4 -Python-2.7.12 intel/2016b 4.0.0 -Python-2.7.13 intel/2017a 4.1.1 -Python-2.7.14 intel/2017b 4.2.0 -Python-2.7.14 foss/2018a 4.2.0 -Python-2.7.14 intel/2018a 4.2.0 -Python-3.6.4 intel/2018a 4.2.5 -Python-2.7.15 foss/2018b 4.2.5 -Python-3.6.6 foss/2018b 4.2.5 -Python-2.7.15 intel/2018b 4.3.3 GCCcore/8.2.0 4.4.2 GCCcore/8.3.0 4.5.2 GCCcore/9.3.0 4.6.2 GCCcore/10.2.0 4.6.3 GCCcore/10.3.0 4.6.3 GCCcore/11.2.0 4.9.1 GCCcore/11.3.0 4.9.2 GCCcore/12.2.0 4.9.2 GCCcore/12.3.0 4.9.3 GCCcore/13.2.0 5.3.0 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/l/lynx/","title":"lynx","text":"lynx is an alphanumeric display oriented World-Wide Web Client
homepage: http://lynx.browser.org/
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","boost":0.5},{"location":"version-specific/supported-software/l/lz4/","title":"lz4","text":"LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core.
homepage: https://lz4.github.io/lz4/
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","boost":0.5},{"location":"version-specific/supported-software/m/","title":"List of supported software (m)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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- MagresPython
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- Maple
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- MariaDB-connector-c
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- memory-profiler
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- meson-python
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- MetaDecoder
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- MetaGeneAnnotator
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- metaWRAP
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- meteogrid
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- MethylDackel
- methylpy
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- MicrobeAnnotator
- microctools
- MiGEC
- MIGRATE-N
- Mikado
- Miller
- mimalloc
- MINC
- MinCED
- Mini-XML
- miniasm
- minibar
- MiniCARD
- Miniconda2
- Miniconda3
- minieigen
- Miniforge3
- Minimac4
- minimap2
- Minipolish
- miniprot
- MiniSat
- minizip
- MINPACK
- MinPath
- MIRA
- miRDeep2
- Mish-Cuda
- misha
- MITgcmutils
- MITObim
- MitoHiFi
- MitoZ
- MiXCR
- MixMHC2pred
- mkl-dnn
- mkl-service
- mkl_fft
- ml-collections
- ml_dtypes
- MLC
- MLflow
- mlpack
- MLxtend
- mm-common
- Mmg
- MMSEQ
- MMseqs2
- mmtf-cpp
- MNE-Python
- MOABB
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- MOB-suite
- ModelTest-NG
- MODFLOW
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- MOKIT
- Molcas
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- molecularGSM
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- MONA
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- MONAI-Label
- mongolite
- Mono
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- MoreRONN
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- motif
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- MotionCor3
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- mpifileutils
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- MySQL-python
- mysqlclient
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/M1QN3/","title":"M1QN3","text":"A solver of large-scale unconstrained minimization problems
homepage: https://who.rocq.inria.fr/Jean-Charles.Gilbert/modulopt/optimization-routines/m1qn3/m1qn3.html
version toolchain 3.3 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/M3GNet/","title":"M3GNet","text":"\" M3GNet is a new materials graph neural network architecture that incorporates 3-body interactions. A key difference with prior materials graph implementations such as MEGNet is the addition of the coordinates for atoms and the 3\u00d73 lattice matrix in crystals, which are necessary for obtaining tensorial quantities such as forces and stresses via auto-differentiation.
homepage: https://materialsvirtuallab.github.io/m3gnet/
version toolchain 0.2.4 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/M4/","title":"M4","text":"GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.
homepage: http://www.gnu.org/software/m4/m4.html
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","boost":0.5},{"location":"version-specific/supported-software/m/MACH/","title":"MACH","text":"MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.
homepage: http://csg.sph.umich.edu/abecasis/MACH/
version toolchain 1.0.18 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MACS2/","title":"MACS2","text":"Model Based Analysis for ChIP-Seq data
homepage: https://github.com/taoliu/MACS/
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","boost":0.5},{"location":"version-specific/supported-software/m/MACS3/","title":"MACS3","text":"Model Based Analysis for ChIP-Seq data
homepage: https://macs3-project.github.io/MACS/
version toolchain 3.0.0 foss/2022b 3.0.0b2 foss/2022b 3.0.1 foss/2022b 3.0.1 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MACSE/","title":"MACSE","text":"MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure.
homepage: https://bioweb.supagro.inra.fr/macse/index.php
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","boost":0.5},{"location":"version-specific/supported-software/m/MAFFT/","title":"MAFFT","text":"MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <\u223c200 sequences), FFT-NS-2 (fast; for alignment of <\u223c10,000 sequences), etc.
homepage: http://mafft.cbrc.jp/alignment/software/
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","boost":0.5},{"location":"version-specific/supported-software/m/MAGIC/","title":"MAGIC","text":"Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm for denoising high-dimensional data most commonly applied to single-cell RNA sequencing data.
homepage: https://krishnaswamylab.org/projects/magic
version toolchain 3.0.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MAGMA-gene-analysis/","title":"MAGMA-gene-analysis","text":"MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis.
homepage: https://ctg.cncr.nl/software/magma
version toolchain 1.07b foss/2018b 1.07bb GCC/8.3.0 1.09b GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MAGeCK/","title":"MAGeCK","text":"Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute, and is being actively updated by Wei Li lab from Children's National Medical Center.
homepage: https://sourceforge.net/p/mageck/wiki/Home/
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","boost":0.5},{"location":"version-specific/supported-software/m/MAJIQ/","title":"MAJIQ","text":"MAJIQ and Voila are two software packages that together detect, quantify, and visualize local splicing variations (LSV) from RNA-Seq data.
homepage: https://majiq.biociphers.org
version versionsuffix toolchain 1.1.1 -Python-3.6.4 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MAKER/","title":"MAKER","text":"MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.
homepage: https://yandell-lab.org/software/maker.html
version toolchain 3.01.04 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MARS/","title":"MARS","text":"improving Multiple circular sequence Alignment using Refined Sequences
homepage: https://github.com/lorrainea/MARS
version toolchain 20191101 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MATES/","title":"MATES","text":"A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data.
homepage: https://github.com/mcgilldinglab/MATES
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","boost":0.5},{"location":"version-specific/supported-software/m/MATIO/","title":"MATIO","text":"matio is an C library for reading and writing Matlab MAT files.
homepage: http://sourceforge.net/projects/matio/
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","boost":0.5},{"location":"version-specific/supported-software/m/MATLAB-Engine/","title":"MATLAB-Engine","text":"The MATLAB Engine API for Python provides a package for Python to call MATLAB as a computational engine.
homepage: https://www.mathworks.com/help/matlab/matlab-engine-for-python.html
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","boost":0.5},{"location":"version-specific/supported-software/m/MATLAB/","title":"MATLAB","text":"MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.
homepage: http://www.mathworks.com/products/matlab
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","boost":0.5},{"location":"version-specific/supported-software/m/MATSim/","title":"MATSim","text":"MATSim is an open-source framework to implement large-scale agent-based transport simulations.
homepage: http://www.matsim.org/
version versionsuffix toolchain 0.8.1 -Java-1.8.0_112 intel/2016b 14.0 -Java-11 GCCcore/11.2.0 14.0 -Java-11 system 15.0 -Java-17 GCCcore/12.3.0 15.0 -Java-17 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MBROLA/","title":"MBROLA","text":"MBROLA is a speech synthesizer based on the concatenation of diphones. It takes a list of phonemes as input, together with prosodic information (duration of phonemes and a piecewise linear description of pitch), and produces speech samples on 16 bits (linear), at the sampling frequency of the diphone database. MBROLA voices project provides list of MBROLA speech synthesizer voices. It is intended to provide easier collaboration and automatic updates for individual users and packagers.
homepage: <['https://github.com/numediart/MBROLA', 'https://github.com/numediart/MBROLA-voices']>
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","boost":0.5},{"location":"version-specific/supported-software/m/MBX/","title":"MBX","text":"MBX is an energy and force calculator for data-driven many-body simulations
homepage: https://github.com/paesanilab/MBX
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","boost":0.5},{"location":"version-specific/supported-software/m/MCL/","title":"MCL","text":"The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.
homepage: http://micans.org/mcl/
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","boost":0.5},{"location":"version-specific/supported-software/m/MCR/","title":"MCR","text":"The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.
homepage: http://www.mathworks.com/products/compiler/mcr/
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","boost":0.5},{"location":"version-specific/supported-software/m/MDAnalysis/","title":"MDAnalysis","text":"MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats.
homepage: https://www.mdanalysis.org/
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","boost":0.5},{"location":"version-specific/supported-software/m/MDBM/","title":"MDBM","text":"MDBM is a super-fast memory-mapped key/value store
homepage: https://github.com/yahoo/mdbm
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","boost":0.5},{"location":"version-specific/supported-software/m/MDI/","title":"MDI","text":"The MolSSI Driver Interface (MDI) project provides a standardized API for fast, on-the-fly communication between computational chemistry codes. This greatly simplifies the process of implementing methods that require the cooperation of multiple software packages and enables developers to write a single implementation that works across many different codes. The API is sufficiently general to support a wide variety of techniques, including QM/MM, ab initio MD, machine learning, advanced sampling, and path integral MD, while also being straightforwardly extensible. Communication between codes is handled by the MDI Library, which enables tight coupling between codes using either the MPI or TCP/IP methods.
homepage: https://github.com/MolSSI-MDI/MDI_Library
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","boost":0.5},{"location":"version-specific/supported-software/m/MDSplus-Java/","title":"MDSplus-Java","text":"MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.
homepage: https://mdsplus.org
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","boost":0.5},{"location":"version-specific/supported-software/m/MDSplus-Python/","title":"MDSplus-Python","text":"MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.
homepage: https://mdsplus.org
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","boost":0.5},{"location":"version-specific/supported-software/m/MDSplus/","title":"MDSplus","text":"MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.
homepage: http://mdsplus.org/
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","boost":0.5},{"location":"version-specific/supported-software/m/MDTraj/","title":"MDTraj","text":"Read, write and analyze MD trajectories with only a few lines of Python code.
homepage: http://mdtraj.org/1.9.0/
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","boost":0.5},{"location":"version-specific/supported-software/m/MEGA/","title":"MEGA","text":"MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an integrated suite of tools for statistics-based comparative analysis of molecular sequence data based on evolutionary principles.
homepage: https://www.megasoftware.net/
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","boost":0.5},{"location":"version-specific/supported-software/m/MEGACC/","title":"MEGACC","text":"MEGA-Computing Core - Sophisticated and user-friendly software suite for analyzing DNA and protein sequence data from species and populations.
homepage: http://www.megasoftware.net
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","boost":0.5},{"location":"version-specific/supported-software/m/MEGAHIT/","title":"MEGAHIT","text":"An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
homepage: https://github.com/voutcn/megahit
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","boost":0.5},{"location":"version-specific/supported-software/m/MEGAN/","title":"MEGAN","text":"MEGAN is a comprehensive toolbox for interactively analyzing microbiome data
homepage: http://megan.informatik.uni-tuebingen.de/
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","boost":0.5},{"location":"version-specific/supported-software/m/MEM/","title":"MEM","text":"Marker Enrichment Modeling (MEM) is a tool designed to calculate enrichment scores.
homepage: https://github.com/cytolab/mem
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","boost":0.5},{"location":"version-specific/supported-software/m/MEME/","title":"MEME","text":"The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo.
homepage: http://meme-suite.org
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","boost":0.5},{"location":"version-specific/supported-software/m/MEMOTE/","title":"MEMOTE","text":"The genome-scale metabolic model test suite
homepage: https://github.com/opencobra/memote
version toolchain 0.13.0 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MERCKX/","title":"MERCKX","text":"Multilingual Entity/Resource Combiner & Knowledge eXtractor
homepage: https://github.com/madewild/MERCKX
version versionsuffix toolchain 20170330 -Python-2.7.13 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MESS/","title":"MESS","text":"Master Equation System Solver (MESS)
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","boost":0.5},{"location":"version-specific/supported-software/m/METIS/","title":"METIS","text":"METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
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","boost":0.5},{"location":"version-specific/supported-software/m/MICOM/","title":"MICOM","text":"Python package to study microbial communities using metabolic modeling.
homepage: https://github.com/micom-dev/micom
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","boost":0.5},{"location":"version-specific/supported-software/m/MIGRATE-N/","title":"MIGRATE-N","text":"Migrate estimates population parameters, effective population sizes and migration rates of n populations, using genetic data. It uses a coalescent theory approach taking into account history of mutations and uncertainty of the genealogy.
homepage: http://popgen.sc.fsu.edu/Migrate/Migrate-n.html
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","boost":0.5},{"location":"version-specific/supported-software/m/MINC/","title":"MINC","text":"Medical Image NetCDF or MINC isn't netCDF.
homepage: https://github.com/BIC-MNI/libminc
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","boost":0.5},{"location":"version-specific/supported-software/m/MINPACK/","title":"MINPACK","text":"Minpack includes software for solving nonlinear equations and nonlinear least squares problems. Five algorithmic paths each include a core subroutine and an easy-to-use driver. The algorithms proceed either from an analytic specification of the Jacobian matrix or directly from the problem functions. The paths include facilities for systems of equations with a banded Jacobian matrix, for least squares problems with a large amount of data, and for checking the consistency of the Jacobian matrix with the functions.
homepage: https://www.netlib.org/minpack/
version toolchain 19961126 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MIRA/","title":"MIRA","text":"MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the latter at the moment only CCS and error-corrected CLR reads).
homepage: http://sourceforge.net/p/mira-assembler/wiki/Home/
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homepage: https://github.com/chrishah/MITObim
version toolchain 1.9.1 foss/2018b 1.9.1 foss/2020b 1.9.1 gompi/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MITgcmutils/","title":"MITgcmutils","text":"A numerical model designed for study of the atmosphere, ocean, and climate, MITgcm\u2019s flexible non-hydrostatic formulation enables it to efficiently simulate fluid phenomena over a wide range of scales; its adjoint capabilities enable it to be applied to sensitivity questions and to parameter and state estimation problems. By employing fluid equation isomorphisms, a single dynamical kernel can be used to simulate flow of both the atmosphere and ocean. The model is developed to perform efficiently on a wide variety of computational platforms.
homepage: https://mitgcm.org/
version toolchain 0.1.2 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MLC/","title":"MLC","text":"Intel Memory Latency Checker (Intel MLC) is a tool used to measure memory latencies and b/w, and how they change with increasing load on the system.
homepage: https://software.intel.com/en-us/articles/intelr-memory-latency-checker
version toolchain 3.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MLflow/","title":"MLflow","text":"MLflow is a platform to streamline machine learning development, including tracking experiments, packaging code into reproducible runs, and sharing and deploying models.
homepage: https://mlflow.org
version toolchain 2.10.2 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MLxtend/","title":"MLxtend","text":"Mlxtend (machine learning extensions) is a Python library of useful tools for the day-to-day data science tasks.
homepage: https://rasbt.github.io/mlxtend/
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","boost":0.5},{"location":"version-specific/supported-software/m/MMSEQ/","title":"MMSEQ","text":"The MMSEQ package contains a collection of statistical tools for analysing RNA-seq expression data.
homepage: https://github.com/eturro/mmseq
version versionsuffix toolchain 1.0.8 -linux64-static system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MMseqs2/","title":"MMseqs2","text":"MMseqs2: ultra fast and sensitive search and clustering suite
homepage: https://github.com/soedinglab/mmseqs2
version toolchain 1-c7a89 foss/2016b 10-6d92c gompi/2019b 10-6d92c iimpi/2019b 11-e1a1c iimpi/2019b 13-45111-20211006 gompi/2020b 13-45111-20211019 gompi/2020b 13-45111 gompi/2020b 13-45111 gompi/2021a 13-45111 gompi/2021b 14-7e284 gompi/2022a 14-7e284 gompi/2023a 5-9375b intel/2018a 8-fac81 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MNE-Python/","title":"MNE-Python","text":"MNE-Python software is an open-source Python package for exploring, visualizing, and analyzing human neurophysiological data such as MEG, EEG, sEEG, ECoG, and more. It includes modules for data input/output, preprocessing, visualization, source estimation, time-frequency analysis, connectivity analysis, machine learning, and statistics.
homepage: https://mne.tools/stable/index.html
version toolchain 0.24.1 foss/2021a 1.6.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MOABB/","title":"MOABB","text":"Build a comprehensive benchmark of popular Brain-Computer Interface (BCI) algorithms applied on an extensive list of freely available EEG datasets.
homepage: https://neurotechx.github.io/moabb/
version toolchain 0.4.6 foss/2021a 1.0.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MOABS/","title":"MOABS","text":"MOABS: MOdel based Analysis of Bisulfite Sequencing data
homepage: https://github.com/sunnyisgalaxy/moabs
version toolchain 1.3.9.6 gompi/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MOB-suite/","title":"MOB-suite","text":"Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
homepage: https://github.com/phac-nml/mob-suite
version versionsuffix toolchain 3.1.0 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MODFLOW/","title":"MODFLOW","text":"MODFLOW is the USGS's modular hydrologic model. MODFLOW is considered an international standard for simulating and predicting groundwater conditions and groundwater/surface-water interactions.
homepage: https://www.usgs.gov/mission-areas/water-resources/science/modflow-and-related-programs
version toolchain 6.4.4 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MOFA2/","title":"MOFA2","text":"MOFA is a factor analysis model that provides a general framework for the integration of multi-omic data sets in an unsupervised fashion. Intuitively, MOFA can be viewed as a versatile and statistically rigorous generalization of principal component analysis to multi-omics data. Given several data matrices with measurements of multiple -omics data types on the same or on overlapping sets of samples, MOFA infers an interpretable low-dimensional representation in terms of a few latent factors. These learnt factors represent the driving sources of variation across data modalities, thus facilitating the identification of cellular states or disease subgroups.
homepage: https://cran.r-project.org/web/packages/rhandsontable/index.html
version versionsuffix toolchain 1.14.0 -R-4.3.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MOKIT/","title":"MOKIT","text":"MOKIT offers various utilities and modules to transfer MOs among various quantum chemistry software packages.
homepage: https://github.com/1234zou/MOKIT
version toolchain 1.2.6_20240830 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MONA/","title":"MONA","text":"MONA is a tool that translates formulas to finite-state automata. The formulas may express search patterns, temporal properties of reactive systems, parse tree constraints, etc. MONA analyses the automaton resulting from the compilation and prints out \"valid\" or a counter-example.
homepage: https://www.brics.dk/mona/index.html
version toolchain 1.4-18 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MONAI-Label/","title":"MONAI-Label","text":"MONAI Label is an intelligent open source image labeling and learning tool that enables users to create annotated datasets and build AI annotation models for clinical evaluation. MONAI Label enables application developers to build labeling apps in a serverless way, where custom labeling apps are exposed as a service through the MONAI Label Server.
homepage: https://docs.monai.io/projects/label/en/latest/
version versionsuffix toolchain 0.5.2 -PyTorch-1.12.0-CUDA-11.7.0 foss/2022a 0.5.2 -PyTorch-1.12.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MONAI/","title":"MONAI","text":"MONAI is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of PyTorch Ecosystem.
homepage: https://monai.io/
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","boost":0.5},{"location":"version-specific/supported-software/m/MOOSE/","title":"MOOSE","text":"The Multiphysics Object-Oriented Simulation Environment (MOOSE) is a finite-element, multiphysics framework primarily developed by Idaho National Laboratory
homepage: https://mooseframework.inl.gov
version versionsuffix toolchain 2021-05-18 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MPB/","title":"MPB","text":"MPB is a free and open-source software package for computing the band structures, or dispersion relations, and electromagnetic modes of periodic dielectric structures, on both serial and parallel computers. MPB is an acronym for MIT Photonic Bands.
homepage: https://mpb.readthedocs.io/en/latest/
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","boost":0.5},{"location":"version-specific/supported-software/m/MPC/","title":"MPC","text":"Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal.
homepage: http://www.multiprecision.org/
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","boost":0.5},{"location":"version-specific/supported-software/m/MPFI/","title":"MPFI","text":"MPFI stands for Multiple Precision Floating-point Interval library.
homepage: https://perso.ens-lyon.fr/nathalie.revol/software.html
version toolchain 1.5.4 GCCcore/11.3.0 1.5.4 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MPFR/","title":"MPFR","text":"The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
homepage: http://www.mpfr.org
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","boost":0.5},{"location":"version-specific/supported-software/m/MPICH/","title":"MPICH","text":"MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).
homepage: http://www.mpich.org/
version toolchain 3.0.4 GCC/4.8.1 3.2 GCC/4.9.3-2.25 3.2 GCC/7.2.0-2.29 3.2.1 GCC/7.2.0-2.29 3.3.2 GCC/10.2.0 3.3.2 GCC/9.3.0 3.4.2 GCC/10.3.0 4.2.1 GCC/12.3.0 4.2.2 GCC/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MPICH2/","title":"MPICH2","text":"MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).
homepage: http://www.mpich.org/
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","boost":0.5},{"location":"version-specific/supported-software/m/MPJ-Express/","title":"MPJ-Express","text":"MPJ Express is an open source Java message passing library that allows application developers to write and execute parallel applications for multicore processors and compute clusters/clouds.
homepage: http://mpj-express.org/
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","boost":0.5},{"location":"version-specific/supported-software/m/MRCPP/","title":"MRCPP","text":"MultiResolution Computation Program Package
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version toolchain 1.3.6 foss/2020a 1.4.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MRChem/","title":"MRChem","text":"MRChem is a numerical real-space code for molecular electronic structure calculations within the self-consistent field (SCF) approximations of quantum chemistry: Hartree-Fock and Density Functional Theory.
homepage: https://mrchem.readthedocs.io
version versionsuffix toolchain 1.0.0 -Python-3.8.2 foss/2020a 1.1.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MRIcron/","title":"MRIcron","text":"MRIcron allows viewing of medical images. It includes tools to complement SPM and FSL. Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images. Features layers, ROIs, and volume rendering.
homepage: http://www.mccauslandcenter.sc.edu/mricro/mricron
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","boost":0.5},{"location":"version-specific/supported-software/m/MRPRESSO/","title":"MRPRESSO","text":"Performs the Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO) method..
homepage: https://github.com/rondolab/MR-PRESSO
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","boost":0.5},{"location":"version-specific/supported-software/m/MRtrix/","title":"MRtrix","text":"MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.
homepage: http://www.brain.org.au/software/index.html#mrtrix
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","boost":0.5},{"location":"version-specific/supported-software/m/MSFragger/","title":"MSFragger","text":"MSFragger is an ultrafast database search tool for peptide identification in mass spectrometry-based proteomics. It has demonstrated excellent performance across a wide range of datasets and applications. MSFragger is suitable for standard shotgun proteomics analyses as well as large datasets (including timsTOF PASEF data), enzyme unconstrained searches (e.g., peptidome), open database searches (e.g., precursor mass tolerance set to hundreds of Daltons) for identification of modified peptides, and glycopeptide identification (N-linked and O-linked).
homepage: https://msfragger.nesvilab.org/
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","boost":0.5},{"location":"version-specific/supported-software/m/MSM/","title":"MSM","text":"Multimodal Surface Matching with Higher order Clique Reduction
homepage: https://github.com/ecr05/MSM_HOCR
version toolchain 1.0 foss/2017b 1.0 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MSPC/","title":"MSPC","text":"Using combined evidence from replicates to evaluate ChIP-seq peaks
homepage: https://genometric.github.io/MSPC/
version toolchain 3.3.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MTL4/","title":"MTL4","text":"The Matrix Template Library 4 incorporates the most modern programming techniques to provide an easy and intuitive interface to users while enabling optimal performance. The natural mathematical notation in MTL4 empowers all engineers and scientists to implement their algorithms and models in minimal time. All technical aspects are encapsulated in the library.
homepage: http://www.simunova.com/mtl4
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","boost":0.5},{"location":"version-specific/supported-software/m/MUMPS/","title":"MUMPS","text":"A parallel sparse direct solver
homepage: http://graal.ens-lyon.fr/MUMPS/
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","boost":0.5},{"location":"version-specific/supported-software/m/MUMmer/","title":"MUMmer","text":"MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.
homepage: http://mummer.sourceforge.net/
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","boost":0.5},{"location":"version-specific/supported-software/m/MUSCLE/","title":"MUSCLE","text":"MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks.
homepage: https://drive5.com/muscle/
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","boost":0.5},{"location":"version-specific/supported-software/m/MUSCLE3/","title":"MUSCLE3","text":"MUSCLE3 allows connecting multiple simulation models together into a multiscale simulation. Simulation models can be as simple as a single Python file, or as complex as a combination of multiple separate simulation codes written in C++ or Fortran, and running on an HPC machine.
homepage: https://muscle3.readthedocs.io/en/latest/index.html
version toolchain 0.7.0 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MUST/","title":"MUST","text":"MUST detects usage errors of the Message Passing Interface (MPI) and reports them to the user. As MPI calls are complex and usage errors common, this functionality is extremely helpful for application developers that want to develop correct MPI applications. This includes errors that already manifest \u2013 segmentation faults or incorrect results \u2013 as well as many errors that are not visible to the application developer or do not manifest on a certain system or MPI implementation.
homepage: https://hpc.rwth-aachen.de/must/
version versionsuffix toolchain 1.6 -Python-3.6.6 foss/2018b 1.6 -Python-3.7.4 foss/2019b 1.7.1 foss/2020b 1.7.2 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MVAPICH2/","title":"MVAPICH2","text":"This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH.
homepage: http://mvapich.cse.ohio-state.edu/overview/mvapich2/
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","boost":0.5},{"location":"version-specific/supported-software/m/MView/","title":"MView","text":"MView reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup.
homepage: https://desmid.github.io/mview/
version toolchain 1.67 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MXNet/","title":"MXNet","text":"Flexible and Efficient Library for Deep Learning
homepage: https://mxnet.io/
version versionsuffix toolchain 0.9.3 -Python-2.7.12-R-3.3.3 foss/2016b 1.9.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MaSuRCA/","title":"MaSuRCA","text":"MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore).
homepage: http://www.genome.umd.edu/masurca.html
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","boost":0.5},{"location":"version-specific/supported-software/m/Magics/","title":"Magics","text":"Magics\u00a0is ECMWF's meteorological plotting software and can be either accessed directly through its Python or\u00a0Fortran interfaces or by using Metview.
homepage: https://confluence.ecmwf.int/display/MAGP/
version toolchain 4.13.0 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MagresPython/","title":"MagresPython","text":"MagresPython is a Python library for parsing the CCP-NC ab-initio magnetic resonance file format. This is used in the latest version of the CASTEP and Quantum ESPRESSO (PWSCF) codes.
homepage: http://tfgg.me/magres-python
version versionsuffix toolchain 20160329 -Python-2.7.15 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Mako/","title":"Mako","text":"A super-fast templating language that borrows the best ideas from the existing templating languages
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homepage: https://mamba.readthedocs.io/
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version toolchain 15 system 2017.2 system 2022.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 0.7.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 10.0.21 GNU/4.9.3-2.25 10.1.13 intel/2016a 10.1.14 foss/2016a 10.1.14 intel/2016a 10.1.17 intel/2016b 10.1.24 intel/2017a 10.11.2 GCC/12.2.0 10.2.11 foss/2017b 10.2.11 intel/2017b 10.3.10 foss/2018b 10.3.14 foss/2019a 10.3.7 intel/2018a 10.4.13 gompi/2019b 10.5.8 GCC/10.2.0 10.6.4 GCC/10.3.0 10.6.4 GCC/11.2.0 10.9.3 GCC/11.3.0 11.6.0 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 3.6 GCCcore/12.2.0 3.6 GCCcore/12.3.0 3.6 GCCcore/13.2.0 3.7 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 2.0 foss/2018a 2.1 foss/2018b 2.2 GCC/9.3.0 2.3 GCC/10.3.0 2.3 GCC/11.2.0 2.3 GCC/11.3.0 2.3 GCC/12.2.0 2.3 GCC/12.3.0 2.3 intel-compilers/2021.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Mashtree/","title":"Mashtree","text":"Create a tree using Mash distances.
homepage: https://github.com/lskatz/mashtree
version toolchain 1.4.6 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: http://mathgl.sourceforge.net/doc_en/Main.html
version toolchain 2.4.1 foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Mathematica/","title":"Mathematica","text":"Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.
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version toolchain 10.0.2 system 10.1.0 system 10.4.1 system 11.0.1 system 11.1.1 system 11.3.0 system 12.0.0 system 12.1.1 system 13.0.0 system 13.1.0 system 9.0.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Maude/","title":"Maude","text":"Maude is a high-performance reflective language and system supporting both equational and rewriting logic specification and programming for a wide range of applications. Maude has been influenced in important ways by the OBJ3 language, which can be regarded as an equational logic sublanguage. Besides supporting equational specification and programming, Maude also supports rewriting logic computation.
homepage: https://maude.cs.illinois.edu/w/index.php/The_Maude_System
version toolchain 3.1 GCCcore/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Maven/","title":"Maven","text":"Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.
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","boost":0.5},{"location":"version-specific/supported-software/m/MaxBin/","title":"MaxBin","text":"MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.
homepage: https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html
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homepage: https://maxquant.org/maxquant/
version toolchain 1.6.10.43 foss/2018b 2.0.3.0 GCCcore/11.2.0 2.2.0.0 GCCcore/11.2.0 2.4.2.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MbedTLS/","title":"MbedTLS","text":"An open source, portable, easy to use, readable and flexible SSL library.
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version toolchain 2.26.0 GCCcore/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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","boost":0.5},{"location":"version-specific/supported-software/m/Meep/","title":"Meep","text":"Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.
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","boost":0.5},{"location":"version-specific/supported-software/m/Meld/","title":"Meld","text":"Meld is a visual diff and merge tool targeted at developers. Meld helps you compare files, directories, and version controlled projects. It provides two- and three-way comparison of both files and directories, and has support for many popular version control systems.
homepage: https://meldmerge.org/
version versionsuffix toolchain 3.20.1 -Python-3.7.2 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Mercurial/","title":"Mercurial","text":"Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface.
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","boost":0.5},{"location":"version-specific/supported-software/m/Mesa-demos/","title":"Mesa-demos","text":"Mesa utility and demo programs, including glxinfo and eglinfo.
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version toolchain 8.4.0 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Mesa/","title":"Mesa","text":"Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
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version toolchain 11.1.2 foss/2016a 11.1.2 gimkl/2.11.5 11.1.2 intel/2016a 11.2.1 foss/2016a 11.2.1 intel/2016a 12.0.2 foss/2016b 12.0.2 intel/2016b 17.0.2 foss/2017a 17.0.2 intel/2017a 17.2.4 intel/2017b 17.2.4 intelcuda/2017b 17.2.5 foss/2017b 17.2.5 fosscuda/2017b 17.3.6 foss/2018a 17.3.6 fosscuda/2018a 17.3.6 intel/2018a 17.3.6 iomkl/2018a 18.1.1 foss/2018b 18.1.1 fosscuda/2018b 18.1.1 intel/2018b 19.0.1 GCCcore/8.2.0 19.1.7 GCCcore/8.3.0 19.2.1 GCCcore/8.3.0 20.0.2 GCCcore/9.3.0 20.2.1 GCCcore/10.2.0 21.1.1 GCCcore/10.3.0 21.1.7 GCCcore/11.2.0 22.0.3 GCCcore/11.3.0 22.2.4 GCCcore/12.2.0 23.1.4 GCCcore/12.3.0 23.1.9 GCCcore/13.2.0 24.1.3 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MeshLab/","title":"MeshLab","text":"The open source mesh processing system.
homepage: https://github.com/cnr-isti-vclab/meshlab
version toolchain 2023.12 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Meson/","title":"Meson","text":"Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
homepage: https://mesonbuild.com
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","boost":0.5},{"location":"version-specific/supported-software/m/Mesquite/","title":"Mesquite","text":"Mesh-Quality Improvement Library
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","boost":0.5},{"location":"version-specific/supported-software/m/MetaBAT/","title":"MetaBAT","text":"An efficient tool for accurately reconstructing single genomes from complex microbial communities
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","boost":0.5},{"location":"version-specific/supported-software/m/MetaDecoder/","title":"MetaDecoder","text":"An algorithm for clustering metagenomic sequences
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version toolchain 1.0.19 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MetaEuk/","title":"MetaEuk","text":"MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.
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version toolchain 4 GCC/10.2.0 5 GCC/10.3.0 6 GCC/11.2.0 6 GCC/11.3.0 6 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MetaGeneAnnotator/","title":"MetaGeneAnnotator","text":"MetaGeneAnnotator is a gene-finding program for prokaryote and phage.
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version versionsuffix toolchain 20080819 -x86-64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MetaMorpheus/","title":"MetaMorpheus","text":"MetaMorpheus is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability. This program combines features of Morpheus and G-PTM-D in a single tool.
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","boost":0.5},{"location":"version-specific/supported-software/m/MetaPhlAn/","title":"MetaPhlAn","text":"MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
homepage: https://github.com/biobakery/MetaPhlAn
version versionsuffix toolchain 3.0.9 -Python-3.8.2 foss/2020a 4.0.6 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MetaPhlAn2/","title":"MetaPhlAn2","text":"MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
homepage: http://huttenhower.sph.harvard.edu/metaphlan2/
version versionsuffix toolchain 2.7.8 -Python-2.7.12 foss/2016b 2.7.8 -Python-3.6.6 foss/2018b 2.7.8 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MetaboAnalystR/","title":"MetaboAnalystR","text":"MetaboAnalystR contains the R functions and libraries underlying the popular MetaboAnalyst web server, including > 500 functions for metabolomic data analysis, visualization, and functional interpretation.
homepage: https://www.metaboanalyst.ca
version versionsuffix toolchain 2.0.1-20190827 -R-3.6.0 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Metagenome-Atlas/","title":"Metagenome-Atlas","text":"Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation.
homepage: https://github.com/metagenome-atlas/atlas
version versionsuffix toolchain 2.4.3 -Python-3.8.2 intel/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Metal/","title":"Metal","text":"Metal - Meta Analysis Helper. The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.
homepage: http://csg.sph.umich.edu/abecasis/Metal/
version toolchain 2011-03-25 foss/2016a 2020-05-05 GCC/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MetalWalls/","title":"MetalWalls","text":"MetalWalls (MW) is a molecular dynamics code dedicated to the modelling of electrochemical systems. Its main originality is the inclusion of a series of methods allowing to apply a constant potential within the electrode materials.
homepage: https://gitlab.com/ampere2/metalwalls
version toolchain 21.06.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Metaxa2/","title":"Metaxa2","text":"Metaxa2 -- Identifies Small Subunit (SSU) rRNAs and classifies them taxonomically
homepage: https://microbiology.se/software/metaxa2/
version toolchain 2.2 gompi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MethylDackel/","title":"MethylDackel","text":"A (mostly) universal methylation extractor for BS-seq experiments.
homepage: https://github.com/dpryan79/MethylDackel
version toolchain 0.4.0 iccifort/2019.1.144-GCC-8.2.0-2.31.1 0.5.0 iccifort/2019.5.281 0.6.1 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MiGEC/","title":"MiGEC","text":"MIGEC is a software pipeline that facilitates processing and analysis of immune repertoire sequencing data generated using molecular barcoding technique
homepage: https://milaboratory.com/software/migec/
version versionsuffix toolchain 1.2.8 -Java-1.8.0_162 system 1.2.9 -Java-1.8 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MiXCR/","title":"MiXCR","text":"MiXCR processes big immunome data from raw sequences to quantitated clonotypes
homepage: https://milaboratory.com/software/mixcr/
version versionsuffix toolchain 2.1.9 -Java-1.8.0_162 system 3.0.13 -Java-1.8 system 3.0.13 -Java-11 system 3.0.3 -Java-1.8 system 4.6.0 -Java-17 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MicrobeAnnotator/","title":"MicrobeAnnotator","text":"Easy-to-use pipeline for the comprehensive metabolic annotation of microbial genomes.
homepage: https://github.com/cruizperez/MicrobeAnnotator
version toolchain 2.0.5 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Mikado/","title":"Mikado","text":"Mikado is a lightweight Python3 pipeline to identify the most useful or \u201cbest\u201d set of transcripts from multiple transcript assemblies. Our approach leverages transcript assemblies generated by multiple methods to define expressed loci, assign a representative transcript and return a set of gene models that selects against transcripts that are chimeric, fragmented or with short or disrupted CDS.
homepage: https://github.com/EI-CoreBioinformatics/mikado
version toolchain 2.3.4 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Miller/","title":"Miller","text":"Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON
homepage: https://miller.readthedocs.io/
version toolchain 6.4.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MinCED/","title":"MinCED","text":"Mining CRISPRs in Environmental Datasets
homepage: https://github.com/ctSkennerton/minced
version versionsuffix toolchain 0.4.2 -Java-11 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MinPath/","title":"MinPath","text":"MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.
homepage: http://omics.informatics.indiana.edu/MinPath
version versionsuffix toolchain 1.4 -Python-2.7.15 foss/2018b 1.4 -Python-2.7.15 intel/2018b 1.4 -Python-2.7.16 intel/2019b 1.6 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Mini-XML/","title":"Mini-XML","text":"Mini-XML is a small XML parsing library that you can use to read XML data files or strings in your application without requiring large non-standard libraries
homepage: https://www.msweet.org/mxml
version toolchain 2.12 GCCcore/9.3.0 2.9 GCCcore/8.2.0 3.2 GCCcore/10.3.0 3.3.1 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MiniCARD/","title":"MiniCARD","text":"MiniCARD is a cardinality solver based on MiniSAT [www.minisat.se]. MiniCARD handles cardinality constraints natively, using the same efficient data structures and techniques MiniSAT uses for clauses, giving it much better performance on cardinality constraints than CNF encodings of those constraints passed to a typical SAT solver. It can read the standard DIMACS CNF format, the OPB pseudo-boolean format (with linear cardinality constraints only), and CNF+, a format that extends CNF to include cardinality constraints.
homepage: https://github.com/liffiton/minicard
version toolchain 1.2 GCC/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MiniSat/","title":"MiniSat","text":"MiniSat is a minimalistic, open-source SAT solver, developed to help researchers and developers alike to get started on SAT.
homepage: http://minisat.se/
version toolchain 2.2.0 GCC/9.3.0 20130925 GCC/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Miniconda2/","title":"Miniconda2","text":"Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages.
homepage: https://docs.conda.io/en/latest/miniconda.html
version toolchain 4.3.21 system 4.6.14 system 4.7.10 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Miniconda3/","title":"Miniconda3","text":"Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages.
homepage: https://docs.conda.io/en/latest/miniconda.html
version toolchain 22.11.1-1 system 23.10.0-1 system 23.5.2-0 system 23.9.0-0 system 4.12.0 system 4.4.10 system 4.5.12 system 4.6.14 system 4.7.10 system 4.8.3 system 4.9.2 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Miniforge3/","title":"Miniforge3","text":"Miniforge is a free minimal installer for conda and Mamba specific to conda-forge.
homepage: https://github.com/conda-forge/miniforge
version toolchain 24.1.2-0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Minimac4/","title":"Minimac4","text":"Minimac4 is a latest version in the series of genotype imputation software - preceded by Minimac3 (2015), Minimac2 (2014), minimac (2012) and MaCH (2010). Minimac4 is a lower memory and more computationally efficient implementation of the original algorithms with comparable imputation quality.
homepage: https://genome.sph.umich.edu/wiki/Minimac4
version toolchain 1.0.0 foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Minipolish/","title":"Minipolish","text":"A tool for Racon polishing of miniasm assemblies
homepage: https://github.com/rrwick/Minipolish
version toolchain 0.1.3 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Mish-Cuda/","title":"Mish-Cuda","text":"Mish-Cuda: Self Regularized Non-Monotonic Activation Function
homepage: https://github.com/JunnYu/mish-cuda
version versionsuffix toolchain 20210309 -PyTorch-1.9.0 fosscuda/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MitoHiFi/","title":"MitoHiFi","text":"MitoHiFi is a Python workflow that assembles mitogenomes from Pacbio HiFi reads
homepage: https://github.com/marcelauliano/MitoHiFi
version toolchain 3.2 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MitoZ/","title":"MitoZ","text":"MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization.
homepage: https://github.com/linzhi2013/MitoZ
version versionsuffix toolchain 2.3 -Python-3.6.6 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MixMHC2pred/","title":"MixMHC2pred","text":"MixMHC2pred is a predictor of HLA class II ligands and epitopes. It is described in publication Racle, J., et al. Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes
homepage: https://github.com/GfellerLab/MixMHC2pred
version toolchain 1.2 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Mmg/","title":"Mmg","text":"Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set of points or from given boundary edges the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries
homepage: https://www.mmgtools.org/
version toolchain 5.3.9 foss/2017b 5.6.0 gompi/2021a 5.6.0 gompi/2021b 5.7.2 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/ModelTest-NG/","title":"ModelTest-NG","text":"ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces.
homepage: https://github.com/ddarriba/modeltest
version toolchain 0.1.7 gompi/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Molcas/","title":"Molcas","text":"Molcas is an ab initio quantum chemistry software package developed by scientists to be used by scientists. The basic philosophy is is to be able to treat general electronic structures for molecules consisting of atoms from most of the periodic table. As such, the primary focus of the package is on multiconfigurational methods with applications typically connected to the treatment of highly degenerate states.
homepage: http://www.molcas.org
version versionsuffix toolchain 8.0-15.06.18 _CentOS_6.6_x86_64 system 8.2 -centos-mkl-par system 8.2 -centos-par system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Molden/","title":"Molden","text":"Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac
homepage: http://www.cmbi.ru.nl/molden/
version toolchain 5.6 foss/2016a 5.7 intel/2016b 5.8 foss/2018a 6.1 GCCcore/8.2.0 6.8 GCCcore/10.2.0 6.8 GCCcore/9.3.0 7.1 GCCcore/11.3.0 7.3 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Molekel/","title":"Molekel","text":"Molekel is an open-source multi-platform molecular visualization program.
homepage: http://ugovaretto.github.io/molekel/wiki/pmwiki.php/Main/HomePage.html
version versionsuffix toolchain 5.4.0 -Linux_x86_64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Molpro/","title":"Molpro","text":"Molpro is a complete system of ab initio programs for molecular electronic structure calculations.
homepage: https://www.molpro.net
version versionsuffix toolchain 2010.1.23 .Linux_x86_64 system 2015.1.0 .linux_x86_64_intel system 2015.1.10 .linux_x86_64_openmp system 2015.1.3 .linux_x86_64_openmp system 2024.1.0 .linux_x86_64_mpipr system 2024.1.0 .linux_x86_64_sockets system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Mono/","title":"Mono","text":"An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
homepage: http://mono-framework.com
version toolchain 2.10.6 intel/2016b 4.6.2.7 intel/2016b 4.6.2.7 system 4.8.0.495 intel/2017a 5.10.0.160 foss/2018a 5.18.1.0 foss/2018a 5.4.1.6 foss/2017b 5.4.1.6 intel/2017b 6.12.0.122 GCCcore/11.2.0 6.4.0.198 foss/2018b 6.8.0.105 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Monocle3/","title":"Monocle3","text":"An analysis toolkit for single-cell RNA-seq.
homepage: https://cole-trapnell-lab.github.io/monocle3/
version versionsuffix toolchain 0.2.0 -Python-3.7.2-R-3.6.0 foss/2019a 0.2.3 -R-4.0.3 foss/2020b 1.3.1 -R-4.2.1 foss/2022a 1.3.1 -R-4.2.2 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MoreRONN/","title":"MoreRONN","text":"MoreRONN is the spiritual successor of RONN and is useful for surveying disorder in proteins as well as designing expressible constructs for X-ray crystallography.
homepage: https://github.com/varun-ramraj/MoreRONN
version toolchain 4.9 GCC/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/Mothur/","title":"Mothur","text":"Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
homepage: http://www.mothur.org/
version versionsuffix toolchain 1.39.5 -Python-2.7.13 intel/2017a 1.41.0 -Python-2.7.15 foss/2018b 1.43.0 -Python-3.7.2 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MotionCor2/","title":"MotionCor2","text":"MotionCor2 correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting. Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, Yifan Cheng and David A. Agard (2016) Anisotropic Correction of Beam-induced Motion for Improved Single-particle Electron Cryo-microscopy, Nature Methods, submitted. BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960
homepage: https://msg.ucsf.edu/
version toolchain 1.2.6 GCCcore/8.2.0 1.3.1 GCCcore/8.3.0 1.3.2 GCCcore/8.3.0 1.4.2 GCCcore/10.2.0 1.4.4 GCCcore/10.2.0 1.4.4 GCCcore/10.3.0 1.5.0 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MotionCor3/","title":"MotionCor3","text":"Anisotropic correction of beam induced motion for cryo-electron microscopy and cryo-electron tomography images. MotionCor3, an improved implementation of MotionCor2 with addition of CTF (Contrast Transfer Function) estimation, is a multi-GPU accelerated software package that enables single-pixel level correction of anisotropic beam induced sample motion for cryo-electron microscopy and cryo-electron tomography images. The iterative, patch-based motion detection combined with spatial and temporal constraints and dose weighting provides robust and accurate correction. By refining the measurement of early motion, MotionCor3 further improves correction on tilted samples. The efficiency achieved by multi-GPU acceleration and parallelization enables correction to keep pace with automated data collection. The recent addition of a very robust GPU-accelerated CTF estimation makes MotionCor3 more versatile in cryoEM and cryoET processing pipeline.
homepage: https://github.com/czimaginginstitute/MotionCor3
version versionsuffix toolchain 1.0.1 -CUDA-12.1.1 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MoviePy/","title":"MoviePy","text":"MoviePy (full documentation) is a Python library for video editing: cutting, concatenations, title insertions, video compositing (a.k.a. non-linear editing), video processing, and creation of custom effects.
homepage: https://zulko.github.io/moviepy/
version versionsuffix toolchain 1.0.1 -Python-3.7.2 foss/2019a 1.0.3 foss/2021a 1.0.3 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/MrBayes/","title":"MrBayes","text":"MrBayes is a program for the Bayesian estimation of phylogeny.
homepage: http://mrbayes.csit.fsu.edu
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","boost":0.5},{"location":"version-specific/supported-software/m/mawk/","title":"mawk","text":"mawk is an interpreter for the AWK Programming Language.
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homepage: https://github.com/dellytools/maze
version toolchain 20170124 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 20191016 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 4.8.13 GCC/4.9.2 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://gitlab.com/janezkonc/mcqd
version toolchain 1.0.0 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 2021-04-06 gomkl/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 1.9.3 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 20150102 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 1.0.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/microctools/","title":"microctools","text":"Various worker functions for microclimc package
homepage: https://github.com/ilyamaclean/microctools
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","boost":0.5},{"location":"version-specific/supported-software/m/mimalloc/","title":"mimalloc","text":"mimalloc is a general purpose allocator with excellent performance characteristics.
homepage: https://microsoft.github.io/mimalloc/
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","boost":0.5},{"location":"version-specific/supported-software/m/miniasm/","title":"miniasm","text":"Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads.
homepage: https://github.com/lh3/minimap2
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","boost":0.5},{"location":"version-specific/supported-software/m/minibar/","title":"minibar","text":"Dual barcode and primer demultiplexing for MinION sequenced reads
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","boost":0.5},{"location":"version-specific/supported-software/m/minieigen/","title":"minieigen","text":"A small wrapper for core parts of EIgen, c++ library for linear algebra.
homepage: https://launchpad.net/minieigen/
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","boost":0.5},{"location":"version-specific/supported-software/m/minimap2/","title":"minimap2","text":"Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment.
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","boost":0.5},{"location":"version-specific/supported-software/m/miniprot/","title":"miniprot","text":"Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Miniprot is similar to GeneWise and Exonerate in functionality but it can map proteins to whole genomes and is much faster at the residue alignment step.
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","boost":0.5},{"location":"version-specific/supported-software/m/minizip/","title":"minizip","text":"Mini zip and unzip based on zlib
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","boost":0.5},{"location":"version-specific/supported-software/m/misha/","title":"misha","text":"The misha package is intended to help users to efficiently analyze genomic data achieved from various experiments.
homepage: https://github.com/tanaylab/misha
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","boost":0.5},{"location":"version-specific/supported-software/m/mkl-dnn/","title":"mkl-dnn","text":"Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN)
homepage: https://01.org/mkl-dnn
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","boost":0.5},{"location":"version-specific/supported-software/m/mkl-service/","title":"mkl-service","text":"Python hooks for Intel(R) Math Kernel Library runtime control settings.
homepage: https://github.com/IntelPython/mkl-service
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","boost":0.5},{"location":"version-specific/supported-software/m/mkl_fft/","title":"mkl_fft","text":"NumPy-based Python interface to Intel(R) MKL FFT functionality
homepage: https://github.com/IntelPython/mkl_fft
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","boost":0.5},{"location":"version-specific/supported-software/m/ml-collections/","title":"ml-collections","text":"ML Collections is a library of Python Collections designed for ML use cases.
homepage: https://github.com/google/ml_collections
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","boost":0.5},{"location":"version-specific/supported-software/m/ml_dtypes/","title":"ml_dtypes","text":"ml_dtypes is a stand-alone implementation of several NumPy dtype extensions used in machine learning libraries, including: bfloat16: an alternative to the standard float16 format float8_*: several experimental 8-bit floating point representations including: float8_e4m3b11fnuz float8_e4m3fn float8_e4m3fnuz float8_e5m2 float8_e5m2fnuz
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","boost":0.5},{"location":"version-specific/supported-software/m/mlpack/","title":"mlpack","text":"mlpack is a fast, header-only C++ machine learning library written in C++ and built on the Armadillo linear algebra library, the ensmallen numerical optimization library, and the cereal serialization library.
homepage: https://www.mlpack.org/
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","boost":0.5},{"location":"version-specific/supported-software/m/mm-common/","title":"mm-common","text":"The mm-common module provides the build infrastructure and utilities shared among the GNOME C++ binding libraries.
homepage: https://gitlab.gnome.org/GNOME/mm-common
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","boost":0.5},{"location":"version-specific/supported-software/m/mmtf-cpp/","title":"mmtf-cpp","text":"The Macromolecular Transmission Format (MMTF) is a new compact binary format to transmit and store biomolecular structures for fast 3D visualization and analysis.
homepage: https://mmtf.rcsb.org/
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","boost":0.5},{"location":"version-specific/supported-software/m/modred/","title":"modred","text":"Compute modal decompositions and reduced-order models, easily, efficiently, and in parallel.
homepage: https://pypi.python.org/pypi/modred/
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","boost":0.5},{"location":"version-specific/supported-software/m/mold/","title":"mold","text":"mold is a high-performance drop-in replacement for existing Unix linkers.
homepage: https://github.com/rui314/mold
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","boost":0.5},{"location":"version-specific/supported-software/m/molecularGSM/","title":"molecularGSM","text":"Code for single-ended and double-ended molecular GSM. The growing string method is a reaction path and transition state finding method developed in c++.
homepage: https://github.com/ZimmermanGroup/molecularGSM
version toolchain 20190826 intel/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/molmod/","title":"molmod","text":"MolMod is a Python library with many compoments that are useful to write molecular modeling programs.
homepage: http://molmod.github.io/molmod/
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","boost":0.5},{"location":"version-specific/supported-software/m/mongolite/","title":"mongolite","text":"High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'. Includes support for aggregation, indexing, map-reduce, streaming, encryption, enterprise authentication, and GridFS. The online user manual provides an overview of the available methods in the package: https://jeroen.github.io/mongolite/.
homepage: https://cran.r-project.org/web/packages/mongolite
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","boost":0.5},{"location":"version-specific/supported-software/m/moonjit/","title":"moonjit","text":"Moonjit is a Just-In-Time Compiler (JIT) for the Lua programming language. Lua is a powerful, dynamic and light-weight programming language. It may be embedded or used as a general-purpose, stand-alone language.
homepage: https://github.com/moonjit/moonjit
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","boost":0.5},{"location":"version-specific/supported-software/m/mordecai/","title":"mordecai","text":"mordecai is a full text geoparsing as a Python library. Extract the place names from a piece of text, resolve them to the correct place, and return their coordinates and structured geographic information.
homepage: https://github.com/openeventdata/mordecai
version versionsuffix toolchain 2.0.1 -Python-3.6.4 foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/morphosamplers/","title":"morphosamplers","text":"A library for sampling image data along morphological objects such as splines and surfaces.
homepage: https://github.com/kevinyamauchi/morphosamplers
version toolchain 0.0.10 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/mosdepth/","title":"mosdepth","text":"Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
homepage: https://github.com/brentp/mosdepth
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","boost":0.5},{"location":"version-specific/supported-software/m/motif/","title":"motif","text":"Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.
homepage: http://motif.ics.com/
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","boost":0.5},{"location":"version-specific/supported-software/m/motionSegmentation/","title":"motionSegmentation","text":"Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation.
homepage: https://github.com/WeiXuanChan/motionSegmentation
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","boost":0.5},{"location":"version-specific/supported-software/m/mpath/","title":"mpath","text":"For now it's quit simple and get_path_info() method returns information about given path. It can be either a directory or a file path.
homepage: https://pypi.org/project/mpath/
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","boost":0.5},{"location":"version-specific/supported-software/m/mpi4py/","title":"mpi4py","text":"MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.
homepage: https://bitbucket.org/mpi4py/mpi4py
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","boost":0.5},{"location":"version-specific/supported-software/m/mpiP/","title":"mpiP","text":"mpiP is a lightweight profiling library for MPI applications. Because it only collects statistical information about MPI functions, mpiP generates considerably less overhead and much less data than tracing tools. All the information captured by mpiP is task-local. It only uses communication during report generation, typically at the end of the experiment, to merge results from all of the tasks into one output file.
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","boost":0.5},{"location":"version-specific/supported-software/m/mpifileutils/","title":"mpifileutils","text":"MPI-Based File Utilities For Distributed Systems
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","boost":0.5},{"location":"version-specific/supported-software/m/mpmath/","title":"mpmath","text":"mpmath can be used as an arbitrary-precision substitute for Python's float/complex types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation can be performed just as well at 10-digit or 1000-digit precision, with either real or complex numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely high precision work.
homepage: http://mpmath.org/
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","boost":0.5},{"location":"version-specific/supported-software/m/mrcfile/","title":"mrcfile","text":"mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. It allows MRC files to be created and opened easily using a very simple API, which exposes the file\u2019s header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested. This library aims to allow users and developers to read and write standard- compliant MRC files in Python as easily as possible, and with no dependencies on any compiled libraries except numpy. You can use it interactively to inspect files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions.
homepage: https://github.com/ccpem/mrcfile
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","boost":0.5},{"location":"version-specific/supported-software/m/msgpack-c/","title":"msgpack-c","text":"MessagePack is an efficient binary serialization format, which lets you exchange data among multiple languages like JSON, except that it's faster and smaller. Small integers are encoded into a single byte while typical short strings require only one extra byte in addition to the strings themselves.
homepage: http://msgpack.org/
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","boost":0.5},{"location":"version-specific/supported-software/m/msprime/","title":"msprime","text":"msprime is a coalescent simulator and library for processing tree-based genetic data.
homepage: https://msprime.readthedocs.io
version versionsuffix toolchain 0.7.0 -Python-3.7.2 intel/2019a 1.2.0 foss/2021b 1.2.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/mstore/","title":"mstore","text":"Molecular structure store for testing
homepage: https://github.com/grimme-lab/mstore
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","boost":0.5},{"location":"version-specific/supported-software/m/muMerge/","title":"muMerge","text":"muMerge is a tool for combining bed regions from multiple bed files that overlap.
homepage: https://github.com/Dowell-Lab/mumerge
version toolchain 1.1.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/muParser/","title":"muParser","text":"muParser is an extensible high performance math expression parser library written in C++. It works by transforming a mathematical expression into bytecode and precalculating constant parts of the expression.
homepage: http://beltoforion.de/article.php?a=muparser
version toolchain 2.2.5 GCCcore/6.4.0 2.3.2 GCCcore/10.2.0 2.3.2 GCCcore/9.3.0 2.3.3 GCCcore/10.3.0 2.3.4 GCCcore/11.3.0 2.3.4 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/mujoco-py/","title":"mujoco-py","text":"MuJoCo is a physics engine for detailed, efficient rigid body simulations with contacts. mujoco-py allows using MuJoCo from Python 3.
homepage: https://github.com/openai/mujoco-py
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homepage: https://github.com/grimme-lab/multicharge
version toolchain 0.2.0 gfbf/2022b 0.2.0 iimkl/2022a 0.2.0 iimkl/2022b 0.3.0 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/m/multichoose/","title":"multichoose","text":"generate multiset combinations (n multichoose k).
homepage: https://github.com/ekg/multichoose
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","boost":0.5},{"location":"version-specific/supported-software/m/multiprocess/","title":"multiprocess","text":"better multiprocessing and multithreading in python
homepage: https://github.com/uqfoundation/multiprocess
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","boost":0.5},{"location":"version-specific/supported-software/m/mumott/","title":"mumott","text":"mumott is a Python library for the analysis of multi-modal tensor tomography data.
homepage: https://mumott.org/
version toolchain 2.1 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://beltoforion.de/en/muparserx/
version toolchain 4.0.8 GCCcore/10.3.0 4.0.8 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: http://people.nas.nasa.gov/~kolano/projects/mutil.html
version toolchain 1.822.3 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://github.com/michaelrsweet/mxml
version toolchain 3.2 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: http://mxml.sourceforge.net
version toolchain 0.9.2 GCC/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://github.com/biothings/mygene.py
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","boost":0.5},{"location":"version-specific/supported-software/m/mympingpong/","title":"mympingpong","text":"A mpi4py based random pair pingpong network stress test.
homepage: https://github.com/hpcugent/mympingpong
version versionsuffix toolchain 0.7.0 -Python-2.7.11 intel/2016a 0.7.1 -Python-2.7.12 intel/2016b 0.8.0 -Python-2.7.15 foss/2019a 0.8.0 -Python-2.7.13 intel/2017a 0.8.0 -Python-2.7.14 intel/2018a 0.8.0 -Python-2.7.15 intel/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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","boost":0.5},{"location":"version-specific/supported-software/m/mysqlclient/","title":"mysqlclient","text":"Python interface to MySQL
homepage: https://github.com/PyMySQL/mysqlclient-python
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","boost":0.5},{"location":"version-specific/supported-software/n/NAGfor/","title":"NAGfor","text":"The checking compiler for improved code portability and detailed error reporting.
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homepage: http://schmidt.chem.wisc.edu/nbosoftware
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homepage: https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html
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homepage: http://www.ncl.ucar.edu
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homepage: https://github.com/xiaochuanle/NECAT
version toolchain 0.0.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/NECI/","title":"NECI","text":"Standalone NECI codebase designed for FCIQMC and other stochastic quantum chemistry methods.
homepage: https://github.com/ghb24/NECI_STABLE
version toolchain 20220711 foss/2022a 20230620 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/NEURON/","title":"NEURON","text":"Empirically-based simulations of neurons and networks of neurons.
homepage: http://www.neuron.yale.edu/neuron
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","boost":0.5},{"location":"version-specific/supported-software/n/NEdit/","title":"NEdit","text":"NEdit is a multi-purpose text editor for the X Window System, which combines a standard, easy to use, graphical user interface with the thorough functionality and stability required by users who edit text eight hours a day.
homepage: http://www.nedit.org
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homepage: https://www-user.tu-chemnitz.de/~potts/nfft/
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homepage: https://ngless.embl.de/
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","boost":0.5},{"location":"version-specific/supported-software/n/NTPoly/","title":"NTPoly","text":"is a massively parallel library for computing the functions of sparse, symmetric matrices based on polynomial expansions. For sufficiently sparse matrices, most of the matrix functions in NTPoly can be computed in linear time.
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homepage: https://nipy.github.io/nibabel
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","boost":0.5},{"location":"version-specific/supported-software/n/Nilearn/","title":"Nilearn","text":"Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.
homepage: https://nilearn.github.io/
version versionsuffix toolchain 0.10.3 gfbf/2023a 0.5.2 -Python-2.7.14 foss/2017b 0.5.2 -Python-3.6.3 foss/2017b 0.5.2 foss/2019a 0.5.2 -Python-2.7.14 intel/2017b 0.5.2 -Python-3.6.3 intel/2017b 0.5.2 intel/2019a 0.7.0 -Python-3.8.2 foss/2020a 0.7.1 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/Nim/","title":"Nim","text":"Nim is a systems and applications programming language.
homepage: https://nim-lang.org/
version toolchain 0.18.0 GCCcore/6.4.0 0.19.2 GCCcore/7.3.0 1.0.0 GCCcore/8.3.0 1.4.6 GCCcore/10.2.0 1.4.8 GCCcore/10.3.0 1.6.6 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/Ninja/","title":"Ninja","text":"Ninja is a small build system with a focus on speed.
homepage: https://ninja-build.org/
version toolchain 1.10.0 GCCcore/9.3.0 1.10.1 GCCcore/10.2.0 1.10.2 GCCcore/10.3.0 1.10.2 GCCcore/11.2.0 1.10.2 GCCcore/11.3.0 1.11.1 GCCcore/12.2.0 1.11.1 GCCcore/12.3.0 1.11.1 GCCcore/13.2.0 1.12.1 GCCcore/13.3.0 1.8.2 foss/2018a 1.8.2 foss/2018b 1.8.2 fosscuda/2018b 1.8.2 intel/2017b 1.8.2 intel/2018a 1.9.0 GCCcore/8.2.0 1.9.0 GCCcore/8.3.0 1.9.0 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/Nipype/","title":"Nipype","text":"Nipype is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow.
homepage: https://nipy.org/nipype
version versionsuffix toolchain 1.0.2 -Python-3.6.4 intel/2018a 1.1.3 -Python-3.6.6 foss/2018b 1.4.2 -Python-3.7.4 intel/2019b 1.6.0 foss/2020b 1.8.5 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/Node-RED/","title":"Node-RED","text":"Node-RED is a programming tool for wiring together hardware devices, APIs and online services in new and interesting ways.
homepage: http://nodered.org
version toolchain 0.16.2 foss/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/Normaliz/","title":"Normaliz","text":"Normaliz is a open source tool for computations in affine monoids, vector configurations, rational polyhedra and rational cones. Normaliz now computes rational and algebraic polyhedra, i.e., polyhedra defined over real algebraic extensions of QQ.
homepage: https://www.normaliz.uni-osnabrueck.de/
version toolchain 3.10.1 gfbf/2022a 3.10.3 gfbf/2023b 3.6.3 intel/2018b 3.7.4 gompi/2019a 3.8.4 GCC/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/Nsight-Compute/","title":"Nsight-Compute","text":"NVIDIA\u00ae Nsight\u2122 Compute is an interactive kernel profiler for CUDA applications. It provides detailed performance metrics and API debugging via a user interface and command line tool. In addition, its baseline feature allows users to compare results within the tool. Nsight Compute provides a customizable and data-driven user interface and metric collection and can be extended with analysis scripts for post-processing results.
homepage: https://developer.nvidia.com/nsight-compute
version toolchain 2020.3.0 system 2021.2.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/Nsight-Systems/","title":"Nsight-Systems","text":"NVIDIA\u00ae Nsight\u2122 Systems is a system-wide performance analysis tool designed to visualize an application\u2019s algorithm, help you select the largest opportunities to optimize, and tune to scale efficiently across any quantity of CPUs and GPUs in your computer; from laptops to DGX servers.
homepage: https://developer.nvidia.com/nsight-compute
version toolchain 2020.5.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/NxTrim/","title":"NxTrim","text":"NxTrim is a software to remove Nextera Mate Pair junction adapters and categorise reads according to the orientation implied by the adapter location.
homepage: https://github.com/sequencing/NxTrim
version toolchain 0.4.3 foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/n2v/","title":"n2v","text":"Noise2Void - Learning Denoising from Single Noisy Images The field of image denoising is currently dominated by discriminative deep learning methods that are trained on pairs of noisy input and clean target images. Recently it has been shown that such methods can also be trained without clean targets. Instead, independent pairs of noisy images can be used, in an approach known as NOISE2NOISE (N2N). Here, we introduce NOISE2VOID (N2V), a training scheme that takes this idea one step further. It does not require noisy image pairs, nor clean target images. Consequently, N2V allows us to train directly on the body of data to be denoised and can therefore be applied when other methods cannot. Especially interesting is the application to biomedical image data, where the acquisition of training targets, clean or noisy, is frequently not possible. We compare the performance of N2V to approaches that have either clean target images and/or noisy image pairs available. Intuitively, N2V cannot be expected to outperform methods that have more information available during training. Still, we observe that the denoising performance of NOISE2VOID drops in moderation and compares favorably to training-free denoising methods.
homepage: https://github.com/juglab/n2v
version versionsuffix toolchain 0.3.2 -CUDA-11.3.1 foss/2021a 0.3.2 foss/2022a 0.3.3 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/namedlist/","title":"namedlist","text":"A Python object, similar to namedtuple, but for lists.
homepage: https://gitlab.com/ericvsmith/namedlist
version toolchain 1.8 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nano/","title":"nano","text":"a simple editor, inspired by Pico
homepage: https://www.nano-editor.org/
version toolchain 6.4 GCCcore/11.3.0 7.0 GCCcore/11.3.0 7.1 GCCcore/12.2.0 7.2 GCCcore/12.2.0 8.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nanoQC/","title":"nanoQC","text":"Quality control tools for long read sequencing data aiming to replicate some of the plots made by fastQC.
homepage: https://github.com/wdecoster/nanoQC
version toolchain 0.9.4 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nanocompore/","title":"nanocompore","text":"Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples
homepage: https://nanocompore.rna.rocks/
version versionsuffix toolchain 1.0.0rc3-2 -Python-3.8.2 intel/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nanoflann/","title":"nanoflann","text":"nanoflann is a C++11 header-only library for building KD-Trees of datasets with different topologies.
homepage: https://github.com/jlblancoc/nanoflann
version toolchain 1.4.0 GCCcore/10.3.0 1.5.0 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nanoget/","title":"nanoget","text":"Functions to extract information from Oxford Nanopore sequencing data and alignments
homepage: https://github.com/wdecoster/nanoget
version versionsuffix toolchain 1.12.1 -Python-3.7.4 intel/2019b 1.15.0 intel/2020b 1.18.1 foss/2021a 1.18.1 foss/2022a 1.18.1 foss/2022b 1.19.1 foss/2022a 1.19.3 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nanomath/","title":"nanomath","text":"A few simple math function for other Oxford Nanopore processing scripts
homepage: https://github.com/wdecoster/nanomath
version versionsuffix toolchain 0.23.1 -Python-3.7.4 intel/2019b 1.2.0 intel/2020b 1.2.1 foss/2021a 1.3.0 foss/2022a 1.3.0 foss/2022b 1.4.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nanomax-analysis-utils/","title":"nanomax-analysis-utils","text":"A set of tools for handling and analysing data at the NanoMAX beamline.
homepage: https://github.com/maxiv-science/nanomax-analysis-utils
version versionsuffix toolchain 0.4 -Python-3.7.4 foss/2019b 0.4 -Python-3.7.4 fosscuda/2019b 0.4.3 foss/2020b 0.4.3 fosscuda/2020b 0.4.4 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nanonet/","title":"nanonet","text":"Nanonet provides recurrent neural network basecalling for Oxford Nanopore MinION data.
homepage: https://github.com/nanoporetech/nanonet
version versionsuffix toolchain 2.0.0 -Python-2.7.13 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nanopolish/","title":"nanopolish","text":"Software package for signal-level analysis of Oxford Nanopore sequencing data.
homepage: https://github.com/jts/nanopolish
version versionsuffix toolchain 0.10.2 -Python-2.7.15 foss/2018b 0.10.2 -Python-2.7.15 intel/2018b 0.13.1 -Python-3.6.6 foss/2018b 0.13.2 -Python-3.8.2 foss/2020a 0.13.3 foss/2020b 0.14.0 foss/2022a 0.14.0 foss/2023a 0.9.2 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/napari-denoiseg/","title":"napari-denoiseg","text":"A napari plugin performing joint denoising and segmentation of microscopy images using DenoiSeg.
homepage: https://juglab.github.io/napari-denoiseg/index.html
version toolchain 0.0.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/napari/","title":"napari","text":"napari is a fast, interactive, multi-dimensional image viewer for Python. It's designed for browsing, annotating, and analyzing large multi-dimensional images. It's built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy).
homepage: https://napari.org/
version toolchain 0.4.15 foss/2021b 0.4.18 foss/2022a 0.4.18 foss/2023a 0.4.19.post1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nauty/","title":"nauty","text":"nauty and Traces are programs for computing automorphism groups of graphs and digraphs. They can also produce a canonical label.
homepage: http://pallini.di.uniroma1.it/
version toolchain 2.6r12 GCC/8.2.0-2.31.1 2.7rc2 GCC/8.2.0-2.31.1 2.7rc5 GCC/8.3.0 2.8.6 GCC/11.3.0 2.8.8 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nbclassic/","title":"nbclassic","text":"NbClassic provides a backwards compatible Jupyter Notebook interface that you can install side-by-side with the latest versions: That way, you can fearlessly upgrade without worrying about your classic extensions and customizations breaking.
homepage: https://jupyter.org/
version toolchain 1.0.0 GCCcore/12.3.0 1.0.0 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/ncbi-vdb/","title":"ncbi-vdb","text":"The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
homepage: https://github.com/ncbi/ncbi-vdb
version toolchain 2.10.4 gompi/2019b 2.10.7 gompi/2020a 2.10.9 gompi/2020b 2.10.9 gompi/2021a 2.11.2 gompi/2021b 2.5.8-1 foss/2016b 2.5.8-1 intel/2016a 2.7.0 foss/2016b 2.8.2 foss/2017b 2.8.2 intel/2017a 2.8.2 intel/2017b 2.9.1-1 foss/2018a 2.9.1-1 intel/2018a 2.9.3 foss/2018b 3.0.0 gompi/2021b 3.0.0 gompi/2022a 3.0.10 gompi/2023a 3.0.2 gompi/2022a 3.0.5 gompi/2021a 3.0.5 gompi/2022b 3.1.1 gompi/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/ncdf4/","title":"ncdf4","text":"ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files
homepage: https://cran.r-project.org/web/packages/ncdf4
version versionsuffix toolchain 1.16 -R-3.4.0 intel/2017a 1.16 -R-3.4.3 intel/2017b 1.16 -R-3.4.4 intel/2018a 1.16.1 -R-3.5.1 foss/2018b 1.16.1 -R-3.6.0 foss/2019a 1.16.1 -R-3.5.1 intel/2018b 1.17 foss/2019b 1.17 -R-4.0.0 foss/2020a 1.17 -R-4.0.3 foss/2020b 1.17 -R-4.1.0 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/ncdu/","title":"ncdu","text":"Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like environment with ncurses installed.
homepage: https://dev.yorhel.nl/ncdu
version toolchain 1.13 GCCcore/7.3.0 1.14 GCCcore/7.3.0 1.15.1 GCCcore/9.3.0 1.16 GCC/10.3.0 1.16 GCC/11.2.0 1.17 GCC/11.3.0 1.18 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/ncolor/","title":"ncolor","text":"Fast remapping of instance labels 1,2,3,...,M to a smaller set of repeating, disjoint labels, 1,2,...,N.
homepage: https://github.com/kevinjohncutler/ncolor
version toolchain 1.2.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/ncompress/","title":"ncompress","text":"Compress is a fast, simple LZW file compressor. Compress does not have the highest compression rate, but it is one of the fastest programs to compress data. Compress is the defacto standard in the UNIX community for compressing files.
homepage: http://ncompress.sourceforge.net/
version toolchain 4.2.4.4 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/ncurses/","title":"ncurses","text":"The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.
homepage: http://www.gnu.org/software/ncurses/
version toolchain 5.9 GCC/4.8.1 5.9 GCC/4.8.2 5.9 GCC/4.8.3 5.9 GCC/4.8.4 5.9 GCC/4.9.2 5.9 GNU/4.9.3-2.25 5.9 gimkl/2.11.5 5.9 system 6.0 GCC/4.9.3-2.25 6.0 GCC/5.4.0-2.26 6.0 GCCcore/4.9.3 6.0 GCCcore/5.3.0 6.0 GCCcore/5.4.0 6.0 GCCcore/6.2.0 6.0 GCCcore/6.3.0 6.0 GCCcore/6.4.0 6.0 GNU/4.9.3-2.25 6.0 foss/2016.04 6.0 foss/2016a 6.0 foss/2016b 6.0 gimkl/2017a 6.0 intel/2016.02-GCC-4.9 6.0 intel/2016a 6.0 intel/2016b 6.0 iomkl/2016.07 6.0 iomkl/2016.09-GCC-4.9.3-2.25 6.0 system 6.1 GCCcore/6.4.0 6.1 GCCcore/7.2.0 6.1 GCCcore/7.3.0 6.1 GCCcore/8.2.0 6.1 GCCcore/8.3.0 6.1 system 6.2 GCCcore/10.2.0 6.2 GCCcore/10.3.0 6.2 GCCcore/11.2.0 6.2 GCCcore/9.3.0 6.2 system 6.3 GCCcore/11.3.0 6.3 GCCcore/12.1.0 6.3 GCCcore/12.2.0 6.3 system 6.4 GCCcore/12.3.0 6.4 GCCcore/13.1.0 6.4 GCCcore/13.2.0 6.4 system 6.5 GCCcore/13.3.0 6.5 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/ncview/","title":"ncview","text":"Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc.
homepage: http://meteora.ucsd.edu/~pierce/ncview_home_page.html
version toolchain 2.1.7 foss/2017b 2.1.7 foss/2018b 2.1.7 foss/2019b 2.1.7 gompi/2019a 2.1.7 intel/2016b 2.1.7 intel/2017a 2.1.7 intel/2017b 2.1.7 intel/2018a 2.1.7 intel/2018b 2.1.7 intel/2019b 2.1.7 iomkl/2018b 2.1.8 gompi/2020a 2.1.8 gompi/2021a 2.1.8 gompi/2021b 2.1.8 gompi/2022a 2.1.8 gompi/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nd2reader/","title":"nd2reader","text":"nd2reader is a pure-Python package that reads images produced by NIS Elements 4.0+.
homepage: https://www.lighthacking.nl/nd2reader/
version versionsuffix toolchain 3.0.6 -Python-2.7.14 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/ne/","title":"ne","text":"ne is a free (GPL'd) text editor based on the POSIX standard that runs (we hope) on almost any UN*X machine. ne is easy to use for the beginner, but powerful and fully configurable for the wizard, and most sparing in its resource usage.
homepage: http://ne.di.unimi.it/
version toolchain 3.0.1 gimkl/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nellie/","title":"nellie","text":"Napari plugin for automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy.
homepage: https://github.com/aelefebv/nellie/
version versionsuffix toolchain 0.3.1 -CUDA-12.1.1 foss/2023a 0.3.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/neon/","title":"neon","text":"neon is an HTTP/1.1 and WebDAV client library, with a C interface.
homepage: https://github.com/notroj/neon
version toolchain 0.31.2 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/neptune-client/","title":"neptune-client","text":"Neptune is an experiment tracking hub that brings organization and collaboration to your data science team.
homepage: https://docs.neptune.ai
version versionsuffix toolchain 0.10.5 foss/2020b 0.16.2 foss/2021a 0.16.2 foss/2022a 0.4.129 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/netCDF-C%2B%2B/","title":"netCDF-C++","text":"NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
homepage: http://www.unidata.ucar.edu/software/netcdf/
version toolchain 4.2 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/netCDF-C%2B%2B4/","title":"netCDF-C++4","text":"NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
homepage: http://www.unidata.ucar.edu/software/netcdf/
version versionsuffix toolchain 4.3.0 foss/2018b 4.3.0 gompi/2019a 4.3.0 iimpi/2019a 4.3.0 intel/2016a 4.3.0 intel/2016b 4.3.0 -HDF5-1.8.18 intel/2017a 4.3.0 intel/2017a 4.3.0 -HDF5-1.8.19 intel/2017b 4.3.0 intel/2018a 4.3.0 intel/2018b 4.3.0 iomkl/2018b 4.3.1 gompi/2019b 4.3.1 gompi/2020a 4.3.1 gompi/2020b 4.3.1 gompi/2021a 4.3.1 gompi/2021b 4.3.1 gompi/2022a 4.3.1 gompi/2023a 4.3.1 gompi/2023b 4.3.1 iimpi/2019b 4.3.1 iimpi/2020a 4.3.1 iimpi/2020b 4.3.1 iimpi/2021a 4.3.1 iimpi/2021b 4.3.1 iimpi/2022a 4.3.1 iimpi/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/netCDF-Fortran/","title":"netCDF-Fortran","text":"NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
homepage: http://www.unidata.ucar.edu/software/netcdf/
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","boost":0.5},{"location":"version-specific/supported-software/n/netCDF/","title":"netCDF","text":"NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
homepage: http://www.unidata.ucar.edu/software/netcdf/
version versionsuffix toolchain 4.3.3.1 foss/2016a 4.3.3.1 intel/2016.02-GCC-4.9 4.3.3.1 intel/2016a 4.4.0 foss/2016a 4.4.0 intel/2016a 4.4.0 iomkl/2016.07 4.4.0 iomkl/2016.09-GCC-4.9.3-2.25 4.4.1 foss/2016a 4.4.1 foss/2016b 4.4.1 intel/2016a 4.4.1 intel/2016b 4.4.1.1 foss/2016b 4.4.1.1 -HDF5-1.10.1 foss/2017a 4.4.1.1 -HDF5-1.8.19 foss/2017a 4.4.1.1 -HDF5-1.8.19 foss/2017b 4.4.1.1 foss/2017b 4.4.1.1 fosscuda/2017b 4.4.1.1 intel/2016b 4.4.1.1 -HDF5-1.10.1 intel/2017a 4.4.1.1 -HDF5-1.8.18 intel/2017a 4.4.1.1 intel/2017a 4.4.1.1 -HDF5-1.8.19 intel/2017b 4.4.1.1 intel/2017b 4.4.1.1 intelcuda/2017b 4.5.0 foss/2017b 4.5.0 intel/2017b 4.5.0 intel/2018.00 4.5.0 intel/2018.01 4.6.0 foss/2018a 4.6.0 intel/2018a 4.6.0 iomkl/2018a 4.6.1 PGI/18.4-GCC-6.4.0-2.28 4.6.1 foss/2018b 4.6.1 fosscuda/2018b 4.6.1 intel/2018b 4.6.1 iomkl/2018b 4.6.2 gompi/2019a 4.6.2 iimpi/2019a 4.7.1 gompi/2019b 4.7.1 gompic/2019b 4.7.1 iimpi/2019b 4.7.1 iimpic/2019b 4.7.4 gompi/2020a 4.7.4 gompi/2020b 4.7.4 gompic/2020a 4.7.4 gompic/2020b 4.7.4 iimpi/2020a 4.7.4 iimpi/2020b 4.7.4 iimpic/2020b 4.7.4 iompi/2020a 4.8.0 gompi/2021a 4.8.0 iimpi/2021a 4.8.1 gompi/2021b 4.8.1 iimpi/2021b 4.9.0 gompi/2022a 4.9.0 gompi/2022b 4.9.0 iimpi/2022a 4.9.0 iimpi/2022b 4.9.2 gompi/2023a 4.9.2 gompi/2023b 4.9.2 iimpi/2023a 4.9.2 iimpi/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/netMHC/","title":"netMHC","text":"NetMHC 4.0 predicts binding of peptides to a number of different HLA alleles using artificial neural networks (ANN).
homepage: https://www.cbs.dtu.dk/services/NetMHC/
version toolchain 4.0a system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/netMHCII/","title":"netMHCII","text":"NetMHCII 2.3 server predicts binding of peptides to HLA-DR, HLA-DQ, HLA-DP and mouse MHC class II alleles using articial neuron networks. Predictions can be obtained for 25 HLA-DR alleles, 20 HLA-DQ, 9 HLA-DP, and 7 mouse H2 class II alleles.
homepage: https://www.cbs.dtu.dk/services/NetMHCII/
version toolchain 2.3 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/netMHCIIpan/","title":"netMHCIIpan","text":"The NetMHCIIpan software predicts binding of peptides to MHC class II molecules. The predictions are available for the three human MHC class II isotypes HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules (H-2).
homepage: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCIIpan
version toolchain 3.2 GCCcore/7.3.0 3.2 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/netMHCpan/","title":"netMHCpan","text":"The NetMHCpan software predicts binding of peptides to any known MHC molecule using artificial neural networks (ANNs).
homepage: https://www.cbs.dtu.dk/services/NetMHCpan/
version toolchain 4.0a system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/netcdf4-python/","title":"netcdf4-python","text":"Python/numpy interface to netCDF.
homepage: https://unidata.github.io/netcdf4-python/
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","boost":0.5},{"location":"version-specific/supported-software/n/netloc/","title":"netloc","text":"The Portable Network Locality (netloc) software package provides network topology discovery tools, and an abstract representation of those networks topologies for a range of network types and configurations. It is provided as a companion to the Portable Hardware Locality (hwloc) package.
homepage: http://www.open-mpi.org/software/netloc
version toolchain 0.5 GCC/4.8.3 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nettle/","title":"nettle","text":"Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space.
homepage: http://www.lysator.liu.se/~nisse/nettle/
version toolchain 3.1.1 GNU/4.9.3-2.25 3.1.1 foss/2016a 3.1.1 intel/2016a 3.10 GCCcore/13.3.0 3.2 GCCcore/5.4.0 3.2 foss/2016b 3.2 intel/2016b 3.3 GCCcore/6.3.0 3.3 GCCcore/6.4.0 3.3 intel/2017a 3.4 GCCcore/6.4.0 3.4 GCCcore/7.3.0 3.4 foss/2018a 3.4 foss/2018b 3.4 fosscuda/2018b 3.4 intel/2018a 3.4 intel/2018b 3.4 iomkl/2018a 3.4.1 GCCcore/8.2.0 3.5.1 GCCcore/8.3.0 3.6 GCCcore/10.2.0 3.6 GCCcore/9.3.0 3.7.2 GCCcore/10.3.0 3.7.3 GCCcore/11.2.0 3.8 GCCcore/11.3.0 3.8.1 GCCcore/12.2.0 3.9.1 GCCcore/12.3.0 3.9.1 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/networkTools/","title":"networkTools","text":"Dynamical Network Analysis is a method of characterizing allosteric signalling through biomolecular complexes.
homepage: http://faculty.scs.illinois.edu/schulten/software/networkTools/
version toolchain 2 GCC/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/networkx/","title":"networkx","text":"NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
homepage: https://pypi.python.org/pypi/networkx
version versionsuffix toolchain 1.1 -Python-2.7.12 intel/2016b 1.11 -Python-2.7.11 foss/2016a 1.11 -Python-3.5.1 foss/2016a 1.11 -Python-2.7.14 intel/2017b 2.0 -Python-2.7.14 intel/2017b 2.1 -Python-2.7.14 intel/2017b 2.2 -Python-2.7.15 foss/2018b 2.2 -Python-3.6.6 foss/2018b 2.2 -Python-2.7.15 foss/2019a 2.2 -Python-2.7.16 foss/2019b 2.2 -Python-2.7.15 intel/2018b 2.2 -Python-3.6.6 intel/2018b 2.3 -Python-3.7.2 foss/2019a 2.3 -Python-3.7.2 intel/2019a 2.4 -Python-3.7.2 foss/2019a 2.4 -Python-3.7.4 foss/2019b 2.4 -Python-3.8.2 foss/2020a 2.4 -Python-3.7.4 fosscuda/2019b 2.4 -Python-3.8.2 fosscuda/2020a 2.4 -Python-3.7.2 intel/2019a 2.4 -Python-3.7.4 intel/2019b 2.4 -Python-3.8.2 intel/2020a 2.4 -Python-3.7.4 intelcuda/2019b 2.5 foss/2020b 2.5 fosscuda/2020b 2.5 intel/2020b 2.5 intelcuda/2020b 2.5.1 foss/2021a 2.6.2 foss/2020b 2.6.3 foss/2021a 2.6.3 foss/2021b 2.6.3 intel/2021b 2.8.4 foss/2022a 2.8.4 intel/2022a 2.8.8 gfbf/2022b 3.0 gfbf/2022b 3.1 gfbf/2023a 3.2.1 gfbf/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nf-core-mag/","title":"nf-core-mag","text":"The Nextflow pipeline 'mag' ported to EasyBuild/EESSI.
homepage: https://nf-co.re/mag
version toolchain 20221110 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nf-core/","title":"nf-core","text":"Python package with helper tools for the nf-core community.
homepage: https://github.com/nf-core/tools
version toolchain 2.10 foss/2022b 2.13.1 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nghttp2/","title":"nghttp2","text":"This is an implementation of the Hypertext Transfer Protocol version 2 in C. The framing layer of HTTP/2 is implemented as a reusable C library. On top of that, we have implemented an HTTP/2 client, server and proxy. We have also developed load test and benchmarking tools for HTTP/2. An HPACK encoder and decoder are available as a public API.
homepage: https://github.com/nghttp2/nghttp2
version toolchain 1.48.0 GCC/11.2.0 1.48.0 GCC/11.3.0 1.58.0 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nghttp3/","title":"nghttp3","text":"nghttp3 is an implementation of RFC 9114 HTTP/3 mapping over QUIC and RFC 9204 QPACK in C. It does not depend on any particular QUIC transport implementation.
homepage: https://github.com/ngtcp2/nghttp3
version toolchain 0.6.0 GCCcore/11.2.0 0.6.0 GCCcore/11.3.0 1.3.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nglview/","title":"nglview","text":"IPython widget to interactively view molecular structures and trajectories.
homepage: https://github.com/arose/nglview
version versionsuffix toolchain 2.7.0 -Python-3.7.2 intel/2019a 2.7.7 -Python-3.8.2 intel/2020a 3.0.3 foss/2021a 3.0.3 foss/2022a 3.1.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/ngspice/","title":"ngspice","text":"Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice.
homepage: https://ngspice.sourceforge.net
version toolchain 31 foss/2019b 39 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/ngtcp2/","title":"ngtcp2","text":"'Call it TCP/2. One More Time.' ngtcp2 project is an effort to implement RFC9000 QUIC protocol.
homepage: https://github.com/ngtcp2/ngtcp2
version toolchain 0.7.0 GCC/11.2.0 0.7.0 GCC/11.3.0 1.2.0 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nichenetr/","title":"nichenetr","text":"R implementation of the NicheNet method, to predict active ligand-target links between interacting cells
homepage: https://github.com/saeyslab/nichenetr
version versionsuffix toolchain 1.1.1-20230223 -R-4.2.1 foss/2022a 2.0.4 -R-4.2.2 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nifti2dicom/","title":"nifti2dicom","text":"Nifti2Dicom is a conversion tool that converts 3D NIfTI files (and other formats supported by ITK, including Analyze, MetaImage Nrrd and VTK) to DICOM. Unlike other conversion tools, it can import a DICOM file that is used to import the patient and study DICOM tags, and allows you to edit the accession number and other DICOM tags, in order to create a valid DICOM that can be imported in a PACS.
homepage: https://github.com/biolab-unige/nifti2dicom
version toolchain 0.4.11 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nifty/","title":"nifty","text":"A nifty library for 2D and 3D image segmentation, graph based segmentation an opt. This library provided building blocks for segmentation algorithms and complex segmentation pipelines.
homepage: https://github.com/DerThorsten/nifty/
version toolchain 1.2.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nlohmann_json/","title":"nlohmann_json","text":"JSON for Modern C++
homepage: https://github.com/nlohmann/json
version toolchain 3.10.0 GCCcore/10.3.0 3.10.4 GCCcore/11.2.0 3.10.5 GCCcore/11.3.0 3.11.2 GCCcore/12.2.0 3.11.2 GCCcore/12.3.0 3.11.3 GCCcore/13.2.0 3.11.3 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nnU-Net/","title":"nnU-Net","text":"nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found in the domain It condenses and automates the keys decisions for designing a successful segmentation pipeline for any given dataset.
homepage: https://github.com/MIC-DKFZ/nnUNet
version toolchain 1.7.0 foss/2020b 1.7.0 fosscuda/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nodejs/","title":"nodejs","text":"Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices.
homepage: http://nodejs.org
version toolchain 10.15.1 foss/2018b 10.15.3 GCCcore/8.2.0 12.16.1 GCCcore/7.3.0 12.16.1 GCCcore/8.3.0 12.16.1 GCCcore/9.3.0 12.19.0 GCCcore/10.2.0 14.17.0 GCCcore/10.3.0 14.17.2 GCCcore/10.3.0 14.17.6 GCCcore/11.2.0 16.15.1 GCCcore/11.3.0 18.12.1 GCCcore/12.2.0 18.17.1 GCCcore/12.3.0 20.13.1 GCCcore/13.3.0 20.9.0 GCCcore/13.2.0 4.4.7 foss/2016a 6.10.3 foss/2017a 8.9.4 foss/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/noise/","title":"noise","text":"Native-code and shader implementations of Perlin noise for Python
homepage: https://github.com/caseman/noise
version toolchain 1.2.2 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nose-parameterized/","title":"nose-parameterized","text":"Parameterized testing with any Python test framework.
homepage: version versionsuffix toolchain 0.5.0 -Python-2.7.11 foss/2016a 0.5.0 -Python-3.5.1 foss/2016a 0.5.0 -Python-3.5.2 intel/2016b 0.6.0 -Python-3.6.1 intel/2017a
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nose3/","title":"nose3","text":"Nose extends unittest to make testing easier.
homepage: https://nose.readthedocs.io/
version toolchain 1.3.8 GCCcore/11.3.0 1.3.8 GCCcore/12.2.0 1.3.8 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/novaSTA/","title":"novaSTA","text":"C++ version of subtomogram averaging (SA) scripts from TOM/AV3 package https://doi.org/10.1073/pnas.0409178102. Both CPU and GPU parallelization is supported although the latter performs significantly worse in terms of processing time (the code is not well optimized) and is thus not recommended for larger datasets.
homepage: https://github.com/turonova/novaSTA
version versionsuffix toolchain 1.1 -CUDA-11.7.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/novoalign/","title":"novoalign","text":"Map short reads onto a reference genome from Illumina, Ion Torrent, and 454 next generation sequencing platforms
homepage: http://www.novocraft.com/products/novoalign/
version versionsuffix toolchain 3.09.00 system 3.09.01 -R-3.5.1 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/npstat/","title":"npstat","text":"npstat implements some population genetics tests and estimators that can be applied to pooled sequences from Next Generation Sequencing experiments.
homepage: https://code.google.com/archive/p/npstat/
version toolchain 0.99 foss/2016a 0.99 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nsync/","title":"nsync","text":"nsync is a C library that exports various synchronization primitives, such as mutexes
homepage: https://github.com/google/nsync
version toolchain 1.24.0 GCCcore/10.2.0 1.24.0 GCCcore/10.3.0 1.24.0 GCCcore/11.2.0 1.24.0 GCCcore/8.3.0 1.24.0 GCCcore/9.3.0 1.25.0 GCCcore/11.3.0 1.26.0 GCCcore/12.2.0 1.26.0 GCCcore/12.3.0 1.29.2 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/ntCard/","title":"ntCard","text":"ntCard is a streaming algorithm for estimating the frequencies of k-mers in genomics datasets.
homepage: https://www.bcgsc.ca/resources/software/ntcard
version toolchain 1.2.1 GCC/11.2.0 1.2.1 GCC/8.3.0 1.2.2 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/ntEdit/","title":"ntEdit","text":"ntEdit is a fast and scalable genomics application for polishing genome assembly drafts.
homepage: https://github.com/bcgsc/ntEdit
version toolchain 1.3.1 iccifort/2018.3.222-GCC-7.3.0-2.30 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/ntHits/","title":"ntHits","text":"ntHits is a method for identifying repeats in high-throughput DNA sequencing data.
homepage: https://github.com/bcgsc/ntHits
version toolchain 0.0.1 iccifort/2018.3.222-GCC-7.3.0-2.30 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/num2words/","title":"num2words","text":"Modules to convert numbers to words. 42 --> forty-two
homepage: https://github.com/savoirfairelinux/num2words
version toolchain 0.5.10 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/numactl/","title":"numactl","text":"The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.
homepage: http://oss.sgi.com/projects/libnuma/
version toolchain 2.0.10 GCC/4.8.4 2.0.10 GCC/4.9.2 2.0.10 GNU/4.9.2-2.25 2.0.10 GNU/4.9.3-2.25 2.0.11 GCC/4.9.3-2.25 2.0.11 GCC/4.9.3 2.0.11 GCC/5.2.0 2.0.11 GCC/5.3.0-2.26 2.0.11 GCC/5.4.0-2.26 2.0.11 GCC/6.1.0-2.27 2.0.11 GCC/6.2.0-2.27 2.0.11 GCC/6.3.0-2.27 2.0.11 GCCcore/4.9.2 2.0.11 GCCcore/4.9.3 2.0.11 GCCcore/5.3.0 2.0.11 GCCcore/5.4.0 2.0.11 GCCcore/6.3.0 2.0.11 GCCcore/6.4.0 2.0.11 GCCcore/7.2.0 2.0.11 GCCcore/7.3.0 2.0.11 foss/2016a 2.0.11 iccifort/2016.3.210-GCC-4.9.3-2.25 2.0.11 iccifort/2016.3.210-GCC-5.4.0-2.26 2.0.11 intel/2016a 2.0.11 intel/2016b 2.0.12 GCCcore/8.2.0 2.0.12 GCCcore/8.3.0 2.0.13 GCCcore/10.2.0 2.0.13 GCCcore/9.2.0 2.0.13 GCCcore/9.3.0 2.0.14 GCCcore/10.3.0 2.0.14 GCCcore/11.2.0 2.0.14 GCCcore/11.3.0 2.0.16 GCCcore/12.2.0 2.0.16 GCCcore/12.3.0 2.0.16 GCCcore/13.2.0 2.0.18 GCCcore/13.3.0 2.0.9 GCC/4.8.3 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/numba/","title":"numba","text":"Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.
homepage: https://numba.pydata.org/
version versionsuffix toolchain 0.24.0 -Python-2.7.11 intel/2016a 0.24.0 -Python-3.5.1 intel/2016a 0.26.0 -Python-2.7.11 intel/2016a 0.32.0 -Python-2.7.13 intel/2017a 0.37.0 -Python-2.7.14 foss/2018a 0.37.0 -Python-3.6.4 foss/2018a 0.37.0 -Python-2.7.14 intel/2017b 0.37.0 -Python-3.6.4 intel/2018a 0.39.0 -Python-3.6.6 foss/2018b 0.43.1 intel/2019a 0.46.0 foss/2019a 0.47.0 -Python-3.7.4 foss/2019b 0.47.0 -Python-3.7.4 fosscuda/2019b 0.50.0 -Python-3.8.2 foss/2020a 0.50.0 -Python-3.8.2 intel/2020a 0.50.1 -Python-3.8.2 foss/2020a 0.52.0 -Python-3.8.2 foss/2020a 0.52.0 foss/2020b 0.52.0 fosscuda/2020b 0.52.0 intel/2020b 0.53.1 foss/2020b 0.53.1 foss/2021a 0.53.1 fosscuda/2020b 0.54.1 -CUDA-11.4.1 foss/2021b 0.54.1 foss/2021b 0.54.1 intel/2021b 0.56.4 -CUDA-11.7.0 foss/2022a 0.56.4 foss/2022a 0.58.1 foss/2022b 0.58.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/numdiff/","title":"numdiff","text":"Numdiff (which I will also write numdiff) is a little program that can be used to compare putatively similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats. Equivalently, Numdiff is a program with the capability to appropriately compare files containing numerical fields (and not only).
homepage: https://www.nongnu.org/numdiff/
version toolchain 5.9.0 GCCcore/10.2.0 5.9.0 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/numexpr/","title":"numexpr","text":"The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a compiler at runtime.
homepage: http://code.google.com/p/numexpr/
version versionsuffix toolchain 2.5.2 -Python-2.7.11 intel/2016a 2.6.1 -Python-2.7.12 foss/2016b 2.6.1 -Python-2.7.12 intel/2016b 2.6.1 -Python-3.5.2 intel/2016b 2.6.4 -Python-3.5.1 foss/2016a 2.6.4 -Python-2.7.13 foss/2017a 2.6.4 -Python-3.6.4 foss/2018a 2.6.4 -Python-3.6.1 intel/2017a 2.6.4 -Python-3.6.3 intel/2017b 2.6.4 -Python-2.7.14 intel/2018a 2.6.4 -Python-3.6.4 intel/2018a 2.6.5 -Python-2.7.15 foss/2018b 2.6.5 -Python-3.6.6 foss/2018b 2.6.5 -Python-3.6.6 fosscuda/2018b 2.6.5 -Python-2.7.15 intel/2018b 2.6.5 -Python-3.6.6 intel/2018b 2.7.0 intel/2019a 2.7.1 -Python-3.7.4 foss/2019b 2.7.1 -Python-3.8.2 foss/2020a 2.7.1 -Python-3.7.4 fosscuda/2019b 2.7.1 -Python-2.7.16 intel/2019b 2.7.1 -Python-3.8.2 intel/2020a 2.8.1 foss/2021a 2.8.1 intel/2021a 2.8.4 foss/2022a 2.9.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/numpy/","title":"numpy","text":"NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.
homepage: http://www.numpy.org
version versionsuffix toolchain 1.10.4 -Python-2.7.11 intel/2016a 1.11.0 -Python-2.7.11 intel/2016a 1.12.1 -Python-3.5.2 intel/2016b 1.13.0 -Python-2.7.13 intel/2017a 1.13.1 -Python-3.6.1 intel/2017a 1.8.2 -Python-2.7.11 foss/2016a 1.8.2 -Python-2.7.11 intel/2016a 1.9.2 -Python-2.7.12 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nvitop/","title":"nvitop","text":"An interactive NVIDIA-GPU process viewer and beyond, the one-stop solution for GPU process management.
homepage: https://nvitop.readthedocs.io.
version versionsuffix toolchain 1.3.2 -CUDA-12.3.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nvofbf/","title":"nvofbf","text":"NVHPC based toolchain, including OpenMPI for MPI support, OpenBLAS (via FlexiBLAS for BLAS and LAPACK support), FFTW and ScaLAPACK.
homepage: <(none)>
version toolchain 2022.07 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nvompi/","title":"nvompi","text":"NVHPC based compiler toolchain, including OpenMPI for MPI support.
homepage: <(none)>
version toolchain 2022.07 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/n/nvtop/","title":"nvtop","text":"htop-like GPU usage monitor
homepage: https://github.com/Syllo/nvtop
version toolchain 1.0.0 fosscuda/2018b 1.1.0 fosscuda/2019b 1.2.1 GCCcore/10.2.0 1.2.1 GCCcore/10.3.0 1.2.2 GCCcore/10.2.0 1.2.2 GCCcore/10.3.0 2.0.2 GCCcore/11.3.0 3.0.1 GCCcore/12.2.0 3.1.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/","title":"List of supported software (o)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- Oases
- OBITools
- OBITools3
- OCaml
- ocamlbuild
- occt
- oceanspy
- OCNet
- Octave
- Octopus-vcf
- OGDF
- olaFlow
- olego
- OMA
- ome-types
- OmegaFold
- OMERO.insight
- OMERO.py
- Omnipose
- onedrive
- ONNX
- ONNX-Runtime
- ont-fast5-api
- ont-guppy
- ont-remora
- OOMPA
- OPARI2
- Open-Data-Cube-Core
- OpenAI-Gym
- openai-python
- OpenBabel
- OpenBLAS
- openCARP
- OpenCensus-python
- OpenCoarrays
- OpenColorIO
- OpenCV
- OpenEXR
- OpenFace
- OpenFAST
- OpenFOAM
- OpenFOAM-Extend
- OpenFold
- OpenForceField
- OpenForceField-Toolkit
- OpenImageIO
- OpenJPEG
- OpenKIM-API
- openkim-models
- OpenMEEG
- OpenMM
- OpenMM-PLUMED
- OpenMMTools
- OpenMolcas
- OpenMPI
- OpenMS
- OpenNLP
- OpenPGM
- OpenPIV
- openpyxl
- OpenRefine
- OpenSceneGraph
- OpenSees
- OpenSlide
- OpenSlide-Java
- openslide-python
- OpenSSL
- OpenStackClient
- OPERA
- OPERA-MS
- OptaDOS
- Optax
- optiSLang
- OptiType
- OptiX
- Optuna
- OR-Tools
- ORCA
- ORFfinder
- OrfM
- orjson
- orthAgogue
- OrthoFinder
- OrthoMCL
- Osi
- OSPRay
- OSU-Micro-Benchmarks
- OTF2
- OVITO
- ownCloud
- oxDNA
- oxford_asl
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OBITools/","title":"OBITools","text":"OBITools is a set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.
homepage: https://git.metabarcoding.org/obitools/obitools/wikis/home
version versionsuffix toolchain 1.2.13 -Python-2.7.15 foss/2019a 1.2.9 -Python-2.7.11 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OBITools3/","title":"OBITools3","text":"A package for the management of analyses and data in DNA metabarcoding.
homepage: https://metabarcoding.org/obitools3
version toolchain 3.0.1b26 GCCcore/12.3.0 3.0.1b8 GCCcore/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OCNet/","title":"OCNet","text":"Generate and analyze Optimal Channel Networks (OCNs): oriented spanning trees reproducing all scaling features characteristic of real, natural river networks. As such, they can be used in a variety of numerical experiments in the fields of hydrology, ecology and epidemiology.
homepage: https://cran.r-project.org/web/packages/OCNet
version versionsuffix toolchain 0.2.0 -R-3.6.0 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OCaml/","title":"OCaml","text":"OCaml is a general purpose industrial-strength programming language with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria it benefits from one of the most advanced type systems and supports functional, imperative and object-oriented styles of programming.
homepage: http://ocaml.org/
version toolchain 4.02.3 foss/2016a 4.07.1 foss/2018b 4.14.0 GCC/11.3.0 5.1.1 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OGDF/","title":"OGDF","text":"OGDF is a self-contained C++ library for graph algorithms, in particular for (but not restricted to) automatic graph drawing. It offers sophisticated algorithms and data structures to use within your own applications or scientific projects.
homepage: https://ogdf.uos.de/
version toolchain dogwood-202202 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OMA/","title":"OMA","text":"The OMA ('Orthologous MAtrix') project is a method and database for the inference of orthologs among complete genomes
homepage: https://omabrowser.org/standalone/
version toolchain 2.1.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OMERO.insight/","title":"OMERO.insight","text":"The OMERO.insight Project is a sub-project of the Open Microscopy Environment Project, OME that focuses on delivering a client for the visualization and manipulation of both image data and metadata maintained at an OMERO server site.
homepage: https://github.com/ome/omero-insight
version versionsuffix toolchain 5.8.3 -Java-11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OMERO.py/","title":"OMERO.py","text":"OMERO.py provides Python bindings to the OMERO.blitz server as well as a pluggable command-line interface.
homepage: https://github.com/ome/omero-py
version toolchain 5.17.0 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/ONNX-Runtime/","title":"ONNX-Runtime","text":"ONNX Runtime inference can enable faster customer experiences and lower costs, supporting models from deep learning frameworks such as PyTorch and TensorFlow/Keras as well as classical machine learning libraries such as scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different hardware, drivers, and operating systems, and provides optimal performance by leveraging hardware accelerators where applicable alongside graph optimizations and transforms.
homepage: https://onnxruntime.ai/
version versionsuffix toolchain 1.10.0 -CUDA-11.3.1 foss/2021a 1.10.0 foss/2021a 1.16.3 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/ONNX/","title":"ONNX","text":"Open Neural Network Exchange (ONNX) is an open ecosystem that empowers AI developers to choose the right tools as their project evolves. ONNX provides an open source format for AI models, both deep learning and traditional ML. It defines an extensible computation graph model, as well as definitions of built-in operators and standard data types. Currently we focus on the capabilities needed for inferencing (scoring).
homepage: https://onnx.ai/
version toolchain 1.11.0 foss/2021a 1.15.0 foss/2022b 1.15.0 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OOMPA/","title":"OOMPA","text":"OOMPA is a suite of R packages for the analysis of gene expression (RNA), proteomics profiling, and other high throughput molecular biology data.
homepage: https://r-forge.r-project.org/projects/oompa
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","boost":0.5},{"location":"version-specific/supported-software/o/OPARI2/","title":"OPARI2","text":"OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface.
homepage: http://www.score-p.org
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","boost":0.5},{"location":"version-specific/supported-software/o/OPERA/","title":"OPERA","text":"An optimal genome scaffolding program
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","boost":0.5},{"location":"version-specific/supported-software/o/OR-Tools/","title":"OR-Tools","text":"Google Optimization Tools (a.k.a., OR-Tools) is an open-source, fast and portable software suite for solving combinatorial optimization problems.
homepage: https://developers.google.com/optimization/
version versionsuffix toolchain 7.1 -Python-3.7.2 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/ORCA/","title":"ORCA","text":"ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
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","boost":0.5},{"location":"version-specific/supported-software/o/ORFfinder/","title":"ORFfinder","text":"ORF finder searches for open reading frames (ORFs) in the DNA sequence you enter. The program returns the range of each ORF, along with its protein translation. Use ORF finder to search newly sequenced DNA for potential protein encoding segments, verify predicted protein using newly developed SMART BLAST or regular BLASTP.
homepage: https://www.ncbi.nlm.nih.gov/orffinder/
version toolchain 0.4.3 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OSPRay/","title":"OSPRay","text":"Open, Scalable, and Portable Ray Tracing Engine
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version toolchain 2.5.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OSU-Micro-Benchmarks/","title":"OSU-Micro-Benchmarks","text":"OSU Micro-Benchmarks
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homepage: http://www.score-p.org
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homepage: https://www.ovito.org
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","boost":0.5},{"location":"version-specific/supported-software/o/Oases/","title":"Oases","text":"Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
homepage: http://www.ebi.ac.uk/~zerbino/oases/
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","boost":0.5},{"location":"version-specific/supported-software/o/Octave/","title":"Octave","text":"GNU Octave is a high-level interpreted language, primarily intended for numerical computations.
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homepage: https://omnipose.readthedocs.io
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","boost":0.5},{"location":"version-specific/supported-software/o/Open-Data-Cube-Core/","title":"Open-Data-Cube-Core","text":"The Open Data Cube Core provides an integrated gridded data analysis environment for decades of analysis ready earth observation satellite and related data from multiple satellite and other acquisition systems.
homepage: https://github.com/opendatacube/datacube-core
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenAI-Gym/","title":"OpenAI-Gym","text":"A toolkit for developing and comparing reinforcement learning algorithms.
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenBabel/","title":"OpenBabel","text":"Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
homepage: http://openbabel.org
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homepage: http://opencv.org/
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homepage: https://opencensus.io/
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homepage: https://github.com/sourceryinstitute/opencoarrays
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenColorIO/","title":"OpenColorIO","text":"OpenColorIO (OCIO) is a complete color management solution geared towards motion picture production with an emphasis on visual effects and computer animation.
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version toolchain 1.1.0 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenFAST/","title":"OpenFAST","text":"OpenFAST is a wind turbine simulation tool which builds on FAST v8. FAST.Farm extends the capability of OpenFAST to simulate multi-turbine wind farms
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version toolchain 3.0.0 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OpenFOAM-Extend/","title":"OpenFOAM-Extend","text":"OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.
homepage: http://www.extend-project.de/
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenFOAM/","title":"OpenFOAM","text":"OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.
homepage: https://www.openfoam.org/
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenFace/","title":"OpenFace","text":"OpenFace \u2013 a state-of-the art tool intended for facial landmark detection, head pose estimation, facial action unit recognition, and eye-gaze estimation.
homepage: https://github.com/TadasBaltrusaitis/OpenFace
version versionsuffix toolchain 2.2.0 -CUDA-11.3.1 foss/2021a 2.2.0 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OpenFold/","title":"OpenFold","text":"A faithful PyTorch reproduction of DeepMind's AlphaFold 2
homepage: https://github.com/aqlaboratory/openfold
version versionsuffix toolchain 1.0.0 -CUDA-11.3.1 foss/2021a 1.0.1 -CUDA-11.3.1 foss/2021a 1.0.1 -CUDA-11.7.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OpenForceField-Toolkit/","title":"OpenForceField-Toolkit","text":"The Open Force Field Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools.
homepage: https://github.com/openforcefield/openff-toolkit
version toolchain 0.16.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OpenForceField/","title":"OpenForceField","text":"Simulation and Parameter Estimation in Geophysics - A python package for simulation and gradient based parameter estimation in the context of geophysical applications.
homepage: https://github.com/openforcefield/openforcefield/releases
version versionsuffix toolchain 0.7.0 -Python-3.8.2 intel/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OpenImageIO/","title":"OpenImageIO","text":"OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications.
homepage: http://openimageio.org/
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenJPEG/","title":"OpenJPEG","text":"OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software.
homepage: http://www.openjpeg.org/
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenKIM-API/","title":"OpenKIM-API","text":"Open Knowledgebase of Interatomic Models. OpenKIM is an API and a collection of interatomic models (potentials) for atomistic simulations. It is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models have to be installed by the user by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all.
homepage: https://openkim.org/
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenMEEG/","title":"OpenMEEG","text":"The OpenMEEG software is a C++ package for solving the forward problems of electroencephalography (EEG) and magnetoencephalography (MEG).
homepage: http://openmeeg.github.io/
version toolchain 2.5.7 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OpenMM-PLUMED/","title":"OpenMM-PLUMED","text":"This project provides a connection between OpenMM and PLUMED. It allows you to bias or analyze an OpenMM simulation based on collective variables.
homepage: https://github.com/openmm/openmm-plumed/
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenMM/","title":"OpenMM","text":"OpenMM is a toolkit for molecular simulation.
homepage: https://simtk.org/home/openmm
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenMMTools/","title":"OpenMMTools","text":"A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine. openmmtools is a Python library layer that sits on top of OpenMM to provide access to a variety of useful tools for building full-featured molecular simulation packages.
homepage: https://github.com/choderalab/openmmtools
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenMPI/","title":"OpenMPI","text":"The Open MPI Project is an open source MPI-2 implementation.
homepage: https://www.open-mpi.org/
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenMS/","title":"OpenMS","text":"As part of the deNBI Center for integrative Bioinformatics, OpenMS offers an open-source software C++ library (+ python bindings) for LC/MS data management and analyses. It provides an infrastructure for the rapid development of mass spectrometry related software as well as a rich toolset built on top of it.
homepage: https://www.openms.de/
version toolchain 2.4.0 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OpenMolcas/","title":"OpenMolcas","text":"OpenMolcas is a quantum chemistry software package
homepage: https://gitlab.com/Molcas/OpenMolcas
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenNLP/","title":"OpenNLP","text":"The Apache OpenNLP library is a machine learning based toolkit for the processing of natural language text.
homepage: https://opennlp.apache.org/
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenPGM/","title":"OpenPGM","text":"OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility.
homepage: https://code.google.com/p/openpgm/
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenPIV/","title":"OpenPIV","text":"OpenPIV is an open source Particle Image Velocimetry analysis software
homepage: http://www.openpiv.net
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenRefine/","title":"OpenRefine","text":"OpenRefine is a power tool that allows you to load data, understand it, clean it up, reconcile it, and augment it with data coming from the web.
homepage: https://github.com/OpenRefine/OpenRefine
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenSSL/","title":"OpenSSL","text":"The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library.
homepage: http://www.openssl.org/
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homepage: http://www.openscenegraph.org/
version toolchain 3.6.5 foss/2021a 3.6.5 foss/2021b 3.6.5 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/o/OpenSees/","title":"OpenSees","text":"Open System for Earthquake Engineering Simulation
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenSlide-Java/","title":"OpenSlide-Java","text":"This is a Java binding to OpenSlide.
homepage: https://github.com/openslide/openslide-java
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","boost":0.5},{"location":"version-specific/supported-software/o/OpenSlide/","title":"OpenSlide","text":"OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides).
homepage: https://openslide.org/
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homepage: https://docs.openstack.org/python-openstackclient/latest/
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homepage: http://www.optados.org/
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","boost":0.5},{"location":"version-specific/supported-software/o/Optax/","title":"Optax","text":"Optax is a gradient processing and optimization library for JAX.
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","boost":0.5},{"location":"version-specific/supported-software/o/OptiType/","title":"OptiType","text":"OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.
homepage: https://github.com/FRED-2/OptiType
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","boost":0.5},{"location":"version-specific/supported-software/o/OptiX/","title":"OptiX","text":"OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPU\u2019s massive ray tracing power using state-of-the-art GPU algorithms.
homepage: https://developer.nvidia.com/optix
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","boost":0.5},{"location":"version-specific/supported-software/o/Optuna/","title":"Optuna","text":"Optuna is an automatic hyperparameter optimization software framework, particularly designed for machine learning. It features an imperative, define-by-run style user API. Thanks to our define-by-run API, the code written with Optuna enjoys high modularity, and the user of Optuna can dynamically construct the search spaces for the hyperparameters.
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homepage: https://www.opencascade.com/
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homepage: https://olaflow.github.io/
version toolchain 20210820 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://github.com/chaolinzhanglab/olego
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homepage: https://github.com/openai/openai-python
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homepage: https://github.com/guyleonard/orthagogue
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- python-docx
- python-elf
- python-hl7
- python-igraph
- python-irodsclient
- python-isal
- python-Levenshtein
- python-libsbml
- python-louvain
- python-mujoco
- python-parasail
- python-telegram-bot
- python-weka-wrapper3
- python-xxhash
- pythran
- PyTorch
- pytorch-3dunet
- PyTorch-bundle
- pytorch-CycleGAN-pix2pix
- PyTorch-Geometric
- PyTorch-Ignite
- PyTorch-Image-Models
- PyTorch-Lightning
- PyTorch3D
- PyTorchVideo
- PyVCF
- PyVCF3
- PyVista
- pyWannier90
- PyWavelets
- PyWBGT
- pyXDF
- PyYAML
- PyZMQ
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PAGAN2/","title":"PAGAN2","text":"PAGAN2 is a general-purpose method for the alignment of DNA, codon and amino-acid sequences as graphs. It aligns sequences either with pileup or, when related by a tree, using phylogeny-aware progressive alignment algorithm. In both cases it uses graphs to describe the uncertainty in the presence of characters at certain sequence positions. PAGAN2 is largely compatible with PAGAN but implements new algorithms for alignment anchoring and memory handling. As a result, PAGAN2 can align sequences of several hundreds of kilobases in length.
homepage: https://github.com/ariloytynoja/pagan2-msa
version versionsuffix toolchain 1.53_20230824 -linux64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PAL2NAL/","title":"PAL2NAL","text":"PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. The program automatically assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the input protein sequence, or contains UTRs, polyA tails. It can also deal with frame shifts in the input alignment, which is suitable for the analysis of pseudogenes. The resulting codon alignment can further be subjected to the calculation of synonymous (d_S) and non-synonymous (d_N) subs- titution rates.
homepage: http://www.bork.embl.de/pal2nal/
version toolchain 14 GCCcore/10.2.0 14 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PALEOMIX/","title":"PALEOMIX","text":"The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data.
homepage: https://github.com/MikkelSchubert/paleomix
version toolchain 1.3.7 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PAML/","title":"PAML","text":"PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
version toolchain 4.10.5 GCCcore/11.3.0 4.9i GCC/6.4.0-2.28 4.9i iccifort/2017.4.196-GCC-6.4.0-2.28 4.9j GCCcore/10.2.0 4.9j GCCcore/10.3.0 4.9j GCCcore/11.2.0 4.9j GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PANDAseq/","title":"PANDAseq","text":"PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
homepage: https://github.com/neufeld/pandaseq
version toolchain 2.10 GCC/5.4.0-2.26 2.10 iccifort/2016.3.210-GCC-5.4.0-2.26 2.11 foss/2017b 2.11 intel/2017b 2.11 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PAPI/","title":"PAPI","text":"PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.
homepage: http://icl.cs.utk.edu/projects/papi/
version toolchain 5.4.3 foss/2016a 5.5.1 GCCcore/6.3.0 5.5.1 GCCcore/6.4.0 5.6.0 GCCcore/6.4.0 5.7.0 GCCcore/7.3.0 5.7.0 GCCcore/8.2.0 6.0.0 GCCcore/10.2.0 6.0.0 GCCcore/8.3.0 6.0.0 GCCcore/9.3.0 6.0.0.1 GCCcore/10.3.0 6.0.0.1 GCCcore/11.2.0 7.0.0 GCCcore/11.3.0 7.0.1 GCCcore/12.2.0 7.0.1 GCCcore/12.3.0 7.1.0 GCCcore/13.2.0 7.1.0 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PARI-GP/","title":"PARI-GP","text":"PARI/GP is a widely used computer algebra system designed for fast computations in number theory (factorizations, algebraic number theory, elliptic curves...), but also contains a large number of other useful functions to compute with mathematical entities such as matrices, polynomials, power series, algebraic numbers etc., and a lot of transcendental functions. PARI is also available as a C library to allow for faster computations.
homepage: https://pari.math.u-bordeaux.fr
version toolchain 2.15.4 GCCcore/11.3.0 2.15.5 GCCcore/13.2.0 2.7.6 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PASA/","title":"PASA","text":"PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.
homepage: https://github.com/PASApipeline/PASApipeline
version toolchain 2.5.3 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PAUP/","title":"PAUP","text":"PAUP (Phylogenetic Analysis Using Parsimony and other methods) is a computational phylogenetics program for inferring evolutionary trees.
homepage: https://paup.phylosolutions.com/
version versionsuffix toolchain 4.0a166 -centos64 system 4.0a168 -centos64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PBSuite/","title":"PBSuite","text":"PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles.
homepage: https://sourceforge.net/p/pb-jelly/wiki/Home/
version versionsuffix toolchain 15.8.24 -Python-2.7.12 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PBZIP2/","title":"PBZIP2","text":"PBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses pthreads and achieves near-linear speedup on SMP machines. The output of this version is fully compatible with bzip2 v1.0.2 or newer (ie: anything compressed with pbzip2 can be decompressed with bzip2). PBZIP2 should work on any system that has a pthreads compatible C++ compiler (such as gcc). It has been tested on: Linux, Windows (cygwin & MinGW), Solaris, Tru64/OSF1, HP-UX, OS/2, OSX, and Irix.
homepage: http://compression.great-site.net/pbzip2
version toolchain 1.1.13 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PCAngsd/","title":"PCAngsd","text":"PCAngsd, which estimates the covariance matrix for low depth NGS data in an iterative procedure based on genotype likelihoods and is able to perform multiple population genetic analyses in heterogeneous populations.
homepage: http://www.popgen.dk/software/index.php/PCAngsd
version versionsuffix toolchain 0.97 -Python-2.7.14 foss/2018a 1.2 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PCC/","title":"PCC","text":"The compiler is based on the original Portable C Compiler by S. C. Johnson, written in the late 70's. About 50% of the frontend code and 80% of the backend code has been modified.
homepage: http://pcc.ludd.ltu.se/
version toolchain 20131024 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PCL/","title":"PCL","text":"The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and point cloud processing.
homepage: http://pointclouds.org/
version versionsuffix toolchain 1.7.2 -Python-2.7.11 intel/2016a 1.8.1 -Python-2.7.14 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PCMSolver/","title":"PCMSolver","text":"An API for the Polarizable Continuum Model.
homepage: https://pcmsolver.readthedocs.org
version versionsuffix toolchain 1.1.4 -Python-2.7.11 intel/2016a 1.2.3 -Python-3.6.6 foss/2018b 1.2.3 -Python-3.7.2 gompi/2019a 1.2.3 -Python-3.7.4 iimpi/2019b 1.2.3 iimpi/2020b 20160205 -Python-2.7.11 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PCRE/","title":"PCRE","text":"The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
homepage: http://www.pcre.org/
version toolchain 8.38 foss/2016a 8.38 foss/2016b 8.38 gimkl/2.11.5 8.38 intel/2016a 8.38 intel/2016b 8.39 GCCcore/5.4.0 8.39 foss/2016b 8.39 intel/2016b 8.40 GCCcore/6.3.0 8.40 gimkl/2017a 8.40 intel/2016b 8.40 intel/2017a 8.41 GCCcore/6.3.0 8.41 GCCcore/6.4.0 8.41 GCCcore/7.3.0 8.42 GCCcore/6.4.0 8.43 GCCcore/8.2.0 8.43 GCCcore/8.3.0 8.44 GCCcore/10.2.0 8.44 GCCcore/10.3.0 8.44 GCCcore/9.3.0 8.45 GCCcore/11.2.0 8.45 GCCcore/11.3.0 8.45 GCCcore/12.2.0 8.45 GCCcore/12.3.0 8.45 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PCRE2/","title":"PCRE2","text":"The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
homepage: http://www.pcre.org/
version toolchain 10.21 foss/2016a 10.31 foss/2018b 10.33 GCCcore/8.2.0 10.33 GCCcore/8.3.0 10.34 GCCcore/9.3.0 10.35 GCCcore/10.2.0 10.36 GCCcore/10.3.0 10.37 GCCcore/11.2.0 10.40 GCCcore/11.3.0 10.40 GCCcore/12.2.0 10.42 GCCcore/12.3.0 10.42 GCCcore/13.2.0 10.43 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PCRaster/","title":"PCRaster","text":"PCRaster Is a collection of software targeted at the development and deployment of spatio-temporal environmental models.
homepage: http://pcraster.geo.uu.nl/
version versionsuffix toolchain 4.1.0 -Python-2.7.14 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PDM/","title":"PDM","text":"A modern Python package and dependency manager supporting the latest PEP standards.
homepage: https://pdm-project.org
version toolchain 2.12.4 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PDT/","title":"PDT","text":"Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations.
homepage: http://www.cs.uoregon.edu/research/pdt/
version toolchain 3.22 foss/2016a 3.25 GCCcore/10.2.0 3.25 GCCcore/8.2.0 3.25 GCCcore/8.3.0 3.25.1 GCCcore/10.3.0 3.25.1 GCCcore/11.2.0 3.25.1 GCCcore/11.3.0 3.25.1 GCCcore/12.2.0 3.25.1 GCCcore/12.3.0 3.25.1 GCCcore/9.3.0 3.25.2 GCCcore/13.2.0 3.25.2 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PEAR/","title":"PEAR","text":"PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.
homepage: http://sco.h-its.org/exelixis/web/software/pear/
version toolchain 0.9.10 GCC/6.4.0-2.28 0.9.10 iccifort/2017.4.196-GCC-6.4.0-2.28 0.9.11 GCC/10.3.0 0.9.11 GCC/11.2.0 0.9.11 GCC/11.3.0 0.9.11 GCCcore/7.3.0 0.9.11 GCCcore/9.3.0 0.9.11 foss/2018a 0.9.8 foss/2016b 0.9.8 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PEPT/","title":"PEPT","text":"A Python library that integrates all the tools necessary to perform research using Positron Emission Particle Tracking (PEPT). The library includes algorithms for the location, identification and tracking of particles, in addition to tools for visualisation and analysis, and utilities allowing the realistic simulation of PEPT data.
homepage: https://pept.readthedocs.io/en/latest/
version toolchain 0.4.1 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PEST%2B%2B/","title":"PEST++","text":"PEST++ is a software suite aimed at supporting complex numerical models in the decision-support context. Much focus has been devoted to supporting environmental models (groundwater, surface water, etc) but these tools are readily applicable to any computer model.
homepage: https://github.com/usgs/pestpp
version toolchain 5.0.5 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PETSc/","title":"PETSc","text":"PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
homepage: https://www.mcs.anl.gov/petsc
version versionsuffix toolchain 3.11.0 -downloaded-deps foss/2018b 3.11.1 -Python-3.7.2 foss/2019a 3.11.1 -Python-3.7.2 intel/2019a 3.12.4 -Python-3.7.4 foss/2019b 3.12.4 -Python-3.8.2 foss/2020a 3.12.4 -Python-2.7.16 intel/2019b 3.12.4 -Python-3.7.4 intel/2019b 3.12.4 -Python-3.8.2 intel/2020a 3.14.4 foss/2020b 3.14.4 intel/2020b 3.15.1 foss/2021a 3.15.1 intel/2021a 3.17.4 foss/2022a 3.18.4 intel/2021b 3.19.2 foss/2022b 3.20.3 foss/2023a 3.7.2 -Python-2.7.11 intel/2016a 3.7.3 -Python-2.7.11 foss/2016a 3.7.5 -downloaded-deps intel/2016b 3.8.3 -downloaded-deps foss/2017b 3.9.1 -downloaded-deps foss/2018a 3.9.3 foss/2018a 3.9.3 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PEcAn/","title":"PEcAn","text":"Ecosystem science, policy, and management informed by the best available data and models.
homepage: https://github.com/PecanProject/pecan
version versionsuffix toolchain 1.8.0.9000 -R-4.3.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PFFT/","title":"PFFT","text":"PFFT is a software library for computing massively parallel, fast Fourier transformations on distributed memory architectures. PFFT can be understood as a generalization of FFTW-MPI to multidimensional data decomposition. The library is written in C and MPI. A Fortran interface is also available. Support for hybrid parallelization based on OpenMP and MPI is under development.
homepage: https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en#pfft
version toolchain 20181230 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PGDSpider/","title":"PGDSpider","text":"An automated data conversion tool for connecting population genetics and genomics programs
homepage: http://cmpg.unibe.ch/software/PGDSpider/
version versionsuffix toolchain 2.1.0.3 -Java-1.7.0_80 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PGI/","title":"PGI","text":"C, C++ and Fortran compilers from The Portland Group - PGI
homepage: http://www.pgroup.com/
version versionsuffix toolchain 15.10 -GCC-4.9.3-2.25 system 15.7 -GNU-4.9.2-2.25 system 15.7 -GNU-4.9.3-2.25 system 16.1 -CDK-GCC-4.9.2-2.25 system 16.10 -GCC-5.4.0-2.26 system 16.3 -GCC-4.9.3-2.25 system 16.4 -GCC-5.3.0-2.26 system 16.7 -GCC-5.4.0-2.26 system 17.1 -GCC-6.3.0-2.27 system 17.10 -GCC-6.4.0-2.28 system 17.3 -GCC-6.3.0-2.28 system 17.4 -GCC-6.4.0-2.28 system 18.1 -GCC-7.2.0-2.29 system 18.10 -GCC-6.4.0-2.28 system 18.4 -GCC-6.4.0-2.28 system 18.7 -GCC-7.3.0-2.30 system 19.1 -GCC-8.2.0-2.31.1 system 19.10 -GCC-8.3.0-2.32 system 19.4 -GCC-8.2.0-2.31.1 system 19.7 -GCC-8.3.0-2.32 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PGPLOT/","title":"PGPLOT","text":"The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time.
homepage: https://sites.astro.caltech.edu/~tjp/pgplot/
version toolchain 5.2.2 GCCcore/11.2.0 5.2.2 GCCcore/11.3.0 5.2.2 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PHANOTATE/","title":"PHANOTATE","text":"PHANOTATE: a tool to annotate phage genomes
homepage: https://github.com/deprekate/PHANOTATE
version toolchain 20190724 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PHASE/","title":"PHASE","text":"The program PHASE implements a Bayesian statistical method for reconstructing haplotypes from population genotype data. Documentation: http://stephenslab.uchicago.edu/assets/software/phase/instruct2.1.pdf
homepage: http://stephenslab.uchicago.edu/phase/download.html
version toolchain 2.1.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PHAST/","title":"PHAST","text":"PHAST is a freely available software package for comparative and evolutionary genomics.
homepage: http://compgen.cshl.edu/phast/
version toolchain 1.4 intel/2017a 1.5 GCC/6.4.0-2.28 1.5 iccifort/2017.4.196-GCC-6.4.0-2.28 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PHLAT/","title":"PHLAT","text":"PHLAT is a bioinformatics algorithm that offers HLA typing at four-digit resolution (or higher) using genome-wide transcriptome and exome sequencing data over a wide range of read lengths and sequencing depths.
homepage: https://sites.google.com/site/phlatfortype/
version versionsuffix toolchain 1.1 -Python-2.7.15 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PHYLIP/","title":"PHYLIP","text":"PHYLIP is a free package of programs for inferring phylogenies.
homepage: http://evolution.genetics.washington.edu/phylip
version toolchain 3.696 foss/2016a 3.696 intel/2016a 3.697 GCC/12.3.0 3.697 GCC/6.4.0-2.28 3.697 GCC/9.3.0 3.697 iccifort/2017.4.196-GCC-6.4.0-2.28 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PICI-LIGGGHTS/","title":"PICI-LIGGGHTS","text":"UoB Positron Imaging Centre's Improved LIGGGHTS distribution with an emphasis on the Python interface.
homepage: https://github.com/uob-positron-imaging-centre/PICI-LIGGGHTS
version toolchain 3.8.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PICRUSt2/","title":"PICRUSt2","text":"PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.
homepage: https://github.com/picrust/picrust2
version toolchain 2.5.2 foss/2022a 2.5.2 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PIL/","title":"PIL","text":"The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities.
homepage: http://www.pythonware.com/products/pil
version versionsuffix toolchain 1.1.7 -Python-2.7.12 foss/2016b 1.1.7 -Python-2.7.15 foss/2019a 1.1.7 -Python-2.7.11-freetype-2.6.3 intel/2016a 1.1.7 -Python-2.7.11 intel/2016a 1.1.7 -Python-2.7.12 intel/2016b 1.1.7 -Python-2.7.13 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PIMS/","title":"PIMS","text":"PIMS is a lazy-loading interface to sequential data with numpy-like slicing.
homepage: https://soft-matter.github.io/pims
version versionsuffix toolchain 0.4.1 -Python-2.7.14 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PIPITS/","title":"PIPITS","text":"An automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences from the Illumina sequencing platform.
homepage: https://github.com/hsgweon/pipits
version versionsuffix toolchain 2.7 -Python-3.8.2 foss/2020a 2.8 foss/2021a 3.0 foss/2021a 3.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PIRATE/","title":"PIRATE","text":"A toolbox for pangenome analysis and threshold evaluation.
homepage: https://github.com/SionBayliss/PIRATE
version versionsuffix toolchain 1.0.5 -R-4.2.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PLAMS/","title":"PLAMS","text":"The Python Library for Automating Molecular Simulation (PLAMS) is powerful and flexible Python tool interfaced to the Amsterdam Modeling Suite engines ADF, BAND, DFTB, MOPAC, ReaxFF, and UFF.
homepage: https://www.scm.com/product/plams
version toolchain 1.5.1 intel/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PLAST/","title":"PLAST","text":"PLAST is a parallel alignment search tool for comparing large protein banks
homepage: http://www.irisa.fr/symbiose/projects/plast/
version versionsuffix toolchain 2.3.1 -Java-1.8.0_92 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PLINK/","title":"PLINK","text":"PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.
homepage: http://zzz.bwh.harvard.edu/plink/
version toolchain 1.07 foss/2016a 1.07 foss/2016b 1.07-x86_64 system 1.90-beta-7.4-x86_64 system 1.9b5 golf/2020a 1.9b_4.1-x86_64 system 1.9b_6.17-x86_64 system 1.9b_6.21-x86_64 system 2.00-alpha1-x86_64 system 2.00-alpha2-x86_64 system 2.00-alpha2-x86_64_avx2 system 2.00a2.3 GCC/10.3.0 2.00a2.3 GCC/11.2.0 2.00a2.3_x86_64 system 2.00a3.1 GCC/11.2.0 2.00a3.6 GCC/11.3.0 2.00a3.7 foss/2022a 2.00a3.7 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PLINKSEQ/","title":"PLINKSEQ","text":"PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.
homepage: https://atgu.mgh.harvard.edu/plinkseq/
version toolchain 0.10 GCC/6.4.0-2.28 0.10 iccifort/2017.4.196-GCC-6.4.0-2.28 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PLUMED/","title":"PLUMED","text":"PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
homepage: http://www.plumed-code.org
version versionsuffix toolchain 2.2.2 intel/2016a 2.2.3 foss/2016b 2.2.3 intel/2016b 2.3.0 foss/2016b 2.3.0 foss/2017a 2.3.0 intel/2016b 2.3.4 intel/2017b 2.4.0 foss/2018a 2.4.0 intel/2017b 2.4.0 -PathCV intel/2018a 2.4.0 intel/2018a 2.4.1 iomkl/2018a 2.4.2 foss/2018b 2.4.2 intel/2018b 2.5.0 -Python-2.7.15 foss/2018b 2.5.0 -Python-2.7.15 fosscuda/2018b 2.5.0 intel/2018b 2.5.1 foss/2019a 2.5.1 -PathCV intel/2018b 2.5.1 intel/2018b 2.5.2 -Python-3.7.2 intel/2019a 2.5.3 -Python-3.7.4 foss/2019b 2.5.3 -Python-3.7.4 intel/2019b 2.5.4 -Python-3.7.4 foss/2019b 2.5.4 -Python-3.7.4 fosscuda/2019b 2.5b -Python-2.7.14 intel/2018a 2.6.0 -Python-3.8.2 foss/2020a 2.6.0 -Python-3.8.2 intel/2020a 2.6.2 foss/2020b 2.6.2 intel/2020b 2.7.0 foss/2020b 2.7.2 foss/2021a 2.7.2 intel/2021a 2.7.3 foss/2021b 2.8.0 foss/2021b 2.8.1 foss/2022a 2.9.0 foss/2022b 2.9.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PLY/","title":"PLY","text":"PLY is yet another implementation of lex and yacc for Python.
homepage: https://www.dabeaz.com/ply/
version versionsuffix toolchain 3.11 GCCcore/12.2.0 3.11 GCCcore/12.3.0 3.11 GCCcore/13.2.0 3.11 GCCcore/13.3.0 3.11 -Python-3.7.4 GCCcore/8.3.0 3.11 -Python-3.6.4 foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PLplot/","title":"PLplot","text":"PLplot is a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer.
homepage: http://plplot.sourceforge.net
version versionsuffix toolchain 5.11.1 -Java-1.7.0_80-Python-2.7.11 foss/2016a 5.11.1 -Java-1.7.0_80-Python-2.7.12 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PMIx/","title":"PMIx","text":"Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to resolve these questions by providing an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability.
homepage: https://pmix.org/
version toolchain 1.2.5 GCCcore/6.4.0 2.1.3 GCCcore/7.2.0 2.1.3 GCCcore/7.3.0 2.2.1 GCCcore/7.2.0 2.2.1 GCCcore/7.3.0 2.2.1 GCCcore/8.2.0 2.2.3 GCCcore/7.2.0 2.2.3 GCCcore/7.3.0 3.0.1 GCCcore/6.4.0 3.0.1 GCCcore/7.3.0 3.0.2 GCCcore/8.2.0 3.0.2 GCCcore/8.3.0 3.1.1 GCCcore/6.4.0 3.1.1 GCCcore/7.3.0 3.1.1 GCCcore/8.2.0 3.1.4 GCCcore/8.3.0 3.1.5 GCCcore/10.2.0 3.1.5 GCCcore/9.3.0 3.2.3 GCCcore/10.3.0 4.1.0 GCCcore/11.2.0 4.1.2 GCCcore/11.3.0 4.2.2 GCCcore/12.2.0 4.2.4 GCCcore/12.3.0 4.2.6 GCCcore/13.2.0 5.0.2 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/POT/","title":"POT","text":"POT (Python Optimal Transport) is a Python library provide several solvers for optimization problems related to Optimal Transport for signal, image processing and machine learning.
homepage: https://github.com/rflamary/POT
version versionsuffix toolchain 0.5.1 -Python-3.6.6 intel/2018b 0.9.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/POV-Ray/","title":"POV-Ray","text":"The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports.
homepage: http://www.povray.org/
version toolchain 3.7.0.0 intel/2016b 3.7.0.10 GCC/11.3.0 3.7.0.10 GCC/12.3.0 3.7.0.7 foss/2017b 3.7.0.7 foss/2018b 3.7.0.7 intel/2017b 3.7.0.7 intel/2018a 3.7.0.7 intel/2018b 3.7.0.8 GCC/10.2.0 3.7.0.8 iccifort/2020.4.304 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PPanGGOLiN/","title":"PPanGGOLiN","text":"PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species.
homepage: https://github.com/labgem/PPanGGOLiN
version toolchain 1.1.136 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PPfold/","title":"PPfold","text":"PPfold is a new implementation of pfold, written in Java 6.0. It can predict the consensus secondary structure of RNA alignments through a stochastic context-free grammar coupled to an evolutionary model. It can also use data from chemical probing experiments to predict RNA secondary structure. PPfold is multithreaded, and can solve the structure of much longer alignments than pfold.
homepage: version versionsuffix toolchain 3.1.1 -Java-1.8.0_66 system
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PRANK/","title":"PRANK","text":"PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events.
homepage: http://wasabiapp.org/software/prank/
version toolchain 170427 GCC/10.2.0 170427 GCC/10.3.0 170427 GCC/11.2.0 170427 GCC/11.3.0 170427 GCC/12.3.0 170427 GCC/9.3.0 170427 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PRC/","title":"PRC","text":"PRC is a stand-alone program for aligning and scoring two profile hidden Markov models. This can be used to detect remote relationships between profiles more effectively than by doing simple profile-sequence comparisons. PRC takes into account all transition and emission probabilities in both hidden Markov models.
homepage:
version toolchain 1.5.6 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PREQUAL/","title":"PREQUAL","text":"A program to identify and mask regions with non-homologous adjacent characters in FASTA files.
homepage: https://github.com/simonwhelan/prequal
version toolchain 1.02 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PRINSEQ/","title":"PRINSEQ","text":"A bioinformatics tool to PRe-process and show INformation of SEQuence data.
homepage: http://prinseq.sourceforge.net
version versionsuffix toolchain 0.20.4 -Perl-5.28.0 foss/2018b 0.20.4 -Perl-5.32.0 foss/2020b 0.20.4 -Perl-5.34.0 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PRISMS-PF/","title":"PRISMS-PF","text":"PRISMS-PF is a powerful, massively parallel finite element code for conducting phase field and other related simulations of microstructural evolution.
homepage: https://prisms-center.github.io/phaseField
version toolchain 2.1.1 foss/2019a 2.1.1 intel/2019a 2.2 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PROJ/","title":"PROJ","text":"Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
homepage: http://trac.osgeo.org/proj/
version toolchain 4.9.2 foss/2016a 4.9.2 foss/2016b 4.9.2 intel/2016a 4.9.2 intel/2016b 4.9.3 foss/2016b 4.9.3 foss/2017b 4.9.3 intel/2016b 4.9.3 intel/2017a 4.9.3 intel/2017b 5.0.0 foss/2018a 5.0.0 foss/2018b 5.0.0 intel/2018a 5.0.0 intel/2018b 5.0.0 iomkl/2018a 6.0.0 GCCcore/8.2.0 6.2.1 GCCcore/8.3.0 6.3.1 GCCcore/10.3.0 7.0.0 GCCcore/9.3.0 7.2.1 GCCcore/10.2.0 8.0.1 GCCcore/10.3.0 8.1.0 GCCcore/11.2.0 9.0.0 GCCcore/11.3.0 9.1.1 GCCcore/12.2.0 9.2.0 GCCcore/12.3.0 9.3.1 GCCcore/13.2.0 9.4.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PRRTE/","title":"PRRTE","text":"PRRTE is the PMIx Reference RunTime Environment
homepage: https://docs.prrte.org/
version toolchain 3.0.5 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PRSice/","title":"PRSice","text":"PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS) analyses.
homepage: https://www.prsice.info/
version toolchain 2.2.12 GCCcore/8.3.0 2.3.1 GCCcore/9.3.0 2.3.3 GCCcore/10.3.0 2.3.3 GCCcore/9.3.0 2.3.5 GCCcore/11.3.0 2.3.5 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PSASS/","title":"PSASS","text":"PSASS (Pooled Sequencing Analysis for Sex Signal) is a software to compare pooled sequencing datasets from two groups (usually two sexes). Results from PSASS can be easily visualized using the sgtr R package. PSASS is integrated in a Snakemake workflow to perform all required steps starting from a genome and reads files.
homepage: https://github.com/SexGenomicsToolkit/PSASS
version toolchain 3.1.0 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PSI/","title":"PSI","text":"PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel.
homepage: http://www.psicode.org/
version versionsuffix toolchain 4.0b6-20160201 -mt-Python-2.7.11 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PSI4/","title":"PSI4","text":"PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel.
homepage: http://www.psicode.org/
version versionsuffix toolchain 1.0 -Python-2.7.11 intel/2016a 1.0 -mt-Python-2.7.11 intel/2016a 1.2.1 -Python-2.7.15-maxam8 intel/2018b 1.2.1 -Python-2.7.15 intel/2018b 1.3.1 -Python-3.7.2 foss/2019a 1.3.2 -Python-3.7.4 intel/2019b 1.7 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PSIPRED/","title":"PSIPRED","text":"Accurate protein secondary structure prediction
homepage: http://bioinf.cs.ucl.ac.uk
version toolchain 4.02 GCC/12.3.0 4.02 GCC/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PSM2/","title":"PSM2","text":"Low-level user-space communications interface for the Intel(R) OPA family of products.
homepage: https://github.com/cornelisnetworks/opa-psm2/
version toolchain 12.0.1 GCCcore/10.3.0 12.0.1 GCCcore/11.2.0 12.0.1 GCCcore/11.3.0 12.0.1 GCCcore/12.2.0 12.0.1 GCCcore/12.3.0 12.0.1 GCCcore/13.2.0 12.0.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PSORTb/","title":"PSORTb","text":"PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.
homepage: http://psort.org/psortb/index.html
version versionsuffix toolchain 3.0.4 -Perl-5.22.1 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PSolver/","title":"PSolver","text":"Poisson Solver from the BigDFT code compiled as a standalone library.
homepage: http://bigdft.org/Wiki/index.php?title=BigDFT_website
version toolchain 1.7.6 foss/2017b 1.7.6 foss/2018a 1.7.6 foss/2018b 1.7.6 intel/2017b 1.7.6 intel/2018a 1.7.6 intel/2018b 1.8.3 foss/2020b 1.8.3 foss/2021a 1.8.3 foss/2021b 1.8.3 intel/2020b 1.8.3 intel/2021a 1.8.3 intel/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PTESFinder/","title":"PTESFinder","text":"Post-Transcriptional Exon Shuffling (PTES) Identification Pipeline
homepage: https://sourceforge.net/projects/ptesfinder-v1/
version toolchain 1 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PYPOWER/","title":"PYPOWER","text":"PYPOWER is a power flow and Optimal Power Flow (OPF) solver. It is a port of MATPOWER to the Python programming language.
homepage: https://github.com/rwl/PYPOWER
version toolchain 5.1.15 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PYTHIA/","title":"PYTHIA","text":"PYTHIA is a standard tool for the generation of events in high-energy collisions, comprising a coherent set of physics models for the evolution from a few-body hard process to a complex multiparticle final state.
homepage: http://home.thep.lu.se/~torbjorn/Pythia.html
version versionsuffix toolchain 8.226 -Python-2.7.13 intel/2017a 8.309 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PaStiX/","title":"PaStiX","text":"PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance parallel solver for very large sparse linear systems based on direct methods.
homepage: http://pastix.gforge.inria.fr/
version toolchain 5.2.3 foss/2017b 6.3.2 foss/2023b 6.3.2 intel/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Pandoc/","title":"Pandoc","text":"If you need to convert files from one markup format into another, pandoc is your swiss-army knife
homepage: http://pandoc.org
version toolchain 2.1.3 system 2.10 system 2.13 system 2.5 system 3.1.2 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Panedr/","title":"Panedr","text":"Panedr uses the Pyedr library to read a Gromacs EDR binary energy XDR file and returns its contents as a pandas dataframe.
homepage: https://github.com/MDAnalysis/panedr
version toolchain 0.7.0 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Pango/","title":"Pango","text":"Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.
homepage: https://www.pango.org/
version toolchain 1.39.0 foss/2016a 1.39.0 intel/2016a 1.40.1 foss/2016a 1.40.1 intel/2016a 1.40.12 intel/2017a 1.40.14 foss/2017b 1.40.14 intel/2017b 1.40.3 foss/2016b 1.40.3 intel/2016b 1.40.5 intel/2017a 1.41.0 foss/2017b 1.41.0 intel/2017b 1.41.1 foss/2018a 1.41.1 intel/2018a 1.42.4 foss/2018b 1.42.4 fosscuda/2018b 1.43.0 GCCcore/8.2.0 1.44.7 GCCcore/8.3.0 1.44.7 GCCcore/9.3.0 1.47.0 GCCcore/10.2.0 1.48.5 GCCcore/10.3.0 1.48.8 GCCcore/11.2.0 1.50.12 GCCcore/12.2.0 1.50.14 GCCcore/12.3.0 1.50.7 GCCcore/11.3.0 1.51.0 GCCcore/13.2.0 1.54.0 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/ParMETIS/","title":"ParMETIS","text":"ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.
homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview
version toolchain 4.0.3 foss/2016a 4.0.3 foss/2016b 4.0.3 foss/2017a 4.0.3 foss/2017b 4.0.3 foss/2018a 4.0.3 foss/2018b 4.0.3 gimkl/2.11.5 4.0.3 gompi/2019a 4.0.3 gompi/2019b 4.0.3 gompi/2020a 4.0.3 gompi/2020b 4.0.3 gompi/2021a 4.0.3 gompi/2021b 4.0.3 gompi/2022a 4.0.3 gompi/2022b 4.0.3 gompi/2023a 4.0.3 gompi/2023b 4.0.3 iimpi/2019a 4.0.3 iimpi/2019b 4.0.3 iimpi/2020a 4.0.3 iimpi/2020b 4.0.3 iimpi/2021a 4.0.3 iimpi/2021b 4.0.3 iimpi/2023b 4.0.3 intel/2016a 4.0.3 intel/2016b 4.0.3 intel/2017a 4.0.3 intel/2017b 4.0.3 intel/2018a 4.0.3 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/ParMGridGen/","title":"ParMGridGen","text":"ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited for geometric multigrid methods.
homepage: http://www-users.cs.umn.edu/~moulitsa/software.html
version toolchain 1.0 gimkl/2.11.5 1.0 gompi/2019b 1.0 gompi/2020a 1.0 iimpi/2019b 1.0 iimpi/2020a 1.0 intel/2016a 1.0 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/ParaView/","title":"ParaView","text":"ParaView is a scientific parallel visualizer.
homepage: http://www.paraview.org
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","boost":0.5},{"location":"version-specific/supported-software/p/Parallel-Hashmap/","title":"Parallel-Hashmap","text":"Parallel Hashmap is built on a modified version of Abseil's flat_hash_map. Parallel Hashmap has lower space requirements, is nearly as fast as the underlying flat_hash_map, and can be used from multiple threads with high levels of concurrency.
homepage: https://github.com/greg7mdp/parallel-hashmap
version toolchain 1.3.12 GCCcore/12.3.0 1.33 GCCcore/10.3.0 1.36 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/ParallelIO/","title":"ParallelIO","text":"A high-level Parallel I/O Library for structured grid applications
homepage: https://github.com/NCAR/ParallelIO
version toolchain 2.2.2a intel/2017a 2.5.10 gompi/2022a 2.5.10 iimpi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Paraver/","title":"Paraver","text":"A very powerful performance visualization and analysis tool based on traces that can be used to analyse any information that is expressed on its input trace format. Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.
homepage: https://tools.bsc.es/paraver
version toolchain 4.11.1 foss/2022a 4.8.1 foss/2019a 4.9.2 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Parcels/","title":"Parcels","text":"Parcels (Probably A Really Computationally Efficient Lagrangian Simulator) is a set of Python classes and methods to create customisable particle tracking simulations using output from Ocean Circulation models. Parcels can be used to track passive and active particulates such as water, plankton, plastic and fish.
homepage: http://www.oceanparcels.org/
version toolchain 2.4.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/ParmEd/","title":"ParmEd","text":"ParmEd is a general tool for aiding in investigations of biomolecular systems using popular molecular simulation packages, like Amber, CHARMM, and OpenMM written in Python.
homepage: http://parmed.github.io/ParmEd/html/index.html
version versionsuffix toolchain 2.7.3 -Python-3.6.3 intel/2017b 3.2.0 -Python-3.7.4 intel/2019b 3.2.0 -Python-3.8.2 intel/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Parsl/","title":"Parsl","text":"Parsl extends parallelism in Python beyond a single computer. You can use Parsl just like Python's parallel executors but across multiple cores and nodes. However, the real power of Parsl is in expressing multi-step workflows of functions. Parsl lets you chain functions together and will launch each function as inputs and computing resources are available.
homepage: https://parsl-project.org/
version toolchain 2023.7.17 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PartitionFinder/","title":"PartitionFinder","text":"PartitionFinder 2 is a Python program for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data. You can PartitionFinder 2 before running a phylogenetic analysis, in order to decide how to divide up your sequence data into separate blocks before analysis, and to simultaneously perform model selection on each of those blocks.
homepage: https://www.robertlanfear.com/partitionfinder
version versionsuffix toolchain 2.1.1 -Python-2.7.18 foss/2020b 2.1.1 -Python-2.7.16 intel/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PennCNV/","title":"PennCNV","text":"A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays.
homepage: https://penncnv.openbioinformatics.org/
version toolchain 1.0.5 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Percolator/","title":"Percolator","text":"Semi-supervised learning for peptide identification from shotgun proteomics datasets
homepage: https://github.com/percolator/percolator
version toolchain 3.4 gompi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Perl-bundle-CPAN/","title":"Perl-bundle-CPAN","text":"A set of common packages from CPAN
homepage: https://www.perl.org/
version toolchain 5.36.1 GCCcore/12.3.0 5.38.0 GCCcore/13.2.0 5.38.2 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Perl/","title":"Perl","text":"Larry Wall's Practical Extraction and Report Language
homepage: http://www.perl.org/
version versionsuffix toolchain 5.20.1 -bare GCC/4.8.2 5.20.1 -bare GCC/4.9.2 5.20.2 -bare GCC/4.9.2 5.20.3 foss/2016a 5.20.3 intel/2016a 5.22.0 -bare GCC/4.9.2 5.22.1 -bare foss/2016a 5.22.1 foss/2016a 5.22.1 foss/2016b 5.22.1 -bare intel/2016a 5.22.1 intel/2016a 5.22.2 intel/2016a 5.24.0 GCC/5.4.0-2.26 5.24.0 GCCcore/4.9.3 5.24.0 GCCcore/5.4.0 5.24.0 -bare foss/2016b 5.24.0 foss/2016b 5.24.0 intel/2016b 5.24.1 GCCcore/6.3.0 5.24.1 foss/2017a 5.24.1 intel/2017a 5.26.0 GCCcore/6.4.0 5.26.0 foss/2017b 5.26.0 intel/2017b 5.26.0 intel/2018.00 5.26.0 intel/2018.01 5.26.1 GCCcore/6.4.0 5.26.1 -bare foss/2018a 5.26.1 foss/2018a 5.28.0 GCCcore/7.3.0 5.28.1 GCCcore/8.2.0 5.30.0 -minimal GCCcore/8.3.0 5.30.0 GCCcore/8.3.0 5.30.2 -minimal GCCcore/9.3.0 5.30.2 GCCcore/9.3.0 5.32.0 -minimal GCCcore/10.2.0 5.32.0 GCCcore/10.2.0 5.32.1 -minimal GCCcore/10.3.0 5.32.1 GCCcore/10.3.0 5.34.0 -minimal GCCcore/11.2.0 5.34.0 GCCcore/11.2.0 5.34.1 -minimal GCCcore/11.3.0 5.34.1 GCCcore/11.3.0 5.36.0 GCCcore/12.1.0 5.36.0 -minimal GCCcore/12.2.0 5.36.0 GCCcore/12.2.0 5.36.1 GCCcore/12.3.0 5.36.1 GCCcore/13.1.0 5.38.0 GCCcore/13.2.0 5.38.0 system 5.38.2 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Perl4-CoreLibs/","title":"Perl4-CoreLibs","text":"Libraries historically supplied with Perl 4
homepage: https://metacpan.org/pod/Perl4::CoreLibs
version versionsuffix toolchain 0.003 -Perl-5.24.1 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Perseus/","title":"Perseus","text":"The Perseus software platform supports biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data.
homepage: https://maxquant.org/perseus
version toolchain 2.0.7.0 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PfamScan/","title":"PfamScan","text":"PfamScan is used to search a FASTA sequence against a library of Pfam HMM.
homepage: https://www.ebi.ac.uk/seqdb/confluence/display/THD/PfamScan
version toolchain 1.6 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Phantompeakqualtools/","title":"Phantompeakqualtools","text":"It computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.
homepage: https://github.com/kundajelab/phantompeakqualtools
version toolchain 1.2.2 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PheWAS/","title":"PheWAS","text":"Provides an accessible R interface to the phenome wide association study.
homepage: https://www.vumc.org/cpm/center-precision-medicine-blog/phewas-r-package
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","boost":0.5},{"location":"version-specific/supported-software/p/PheWeb/","title":"PheWeb","text":"A tool for building PheWAS websites from association files
homepage: https://github.com/statgen/pheweb
version versionsuffix toolchain 1.1.20 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Phenoflow/","title":"Phenoflow","text":"R package offering functionality for the advanced analysis of microbial flow cytometry data
homepage: https://github.com/rprops/Phenoflow_package
version versionsuffix toolchain 1.1.2-20200917 -R-4.2.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PhiPack/","title":"PhiPack","text":"The PhiPack software package implements (in C) a few tests for recombination and can produce refined incompatibility matrices as well.
homepage: http://www.maths.otago.ac.nz/~dbryant/software.html
version toolchain 2016.06.14 iccifort/2019.1.144-GCC-8.2.0-2.31.1 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Philosopher/","title":"Philosopher","text":"Philosopher is a fast, easy-to-use, scalable, and versatile data analysis software for mass spectrometry-based proteomics. Philosopher is dependency-free and can analyze both traditional database searches and open searches for post-translational modification (PTM) discovery.
homepage: https://philosopher.nesvilab.org/
version toolchain 5.0.0 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PhyML/","title":"PhyML","text":"Phylogenetic estimation using (Maximum) Likelihood
homepage: https://github.com/stephaneguindon/phyml
version toolchain 3.3.20190321 foss/2018b 3.3.20200621 foss/2020b 3.3.20220408 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PhyloBayes-MPI/","title":"PhyloBayes-MPI","text":"A Bayesian software for phylogenetic reconstruction using mixture models
homepage: https://github.com/bayesiancook/pbmpi
version toolchain 20161021 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PhyloPhlAn/","title":"PhyloPhlAn","text":"PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution.
homepage: https://github.com/biobakery/phylophlan
version versionsuffix toolchain 3.0 -Python-3.8.2 foss/2020a 3.0.2 foss/2021a 3.0.3 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PileOMeth/","title":"PileOMeth","text":"PileOMeth processes a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments. PileOMeth extracts per-base methylation metrics from them. PileOMeth requires an indexed fasta file containing the reference genome as well.
homepage: https://github.com/dpryan79/PileOMeth
version toolchain 0.1.11 foss/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Pillow-SIMD/","title":"Pillow-SIMD","text":"Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
homepage: https://github.com/uploadcare/pillow-simd
version versionsuffix toolchain 10.4.0 GCCcore/13.3.0 5.0.0 -Python-3.6.4 foss/2018a 5.0.0 -Python-3.6.4 intel/2018a 5.3.0.post0 -Python-3.6.6 foss/2018b 5.3.0.post0 -Python-3.6.6 fosscuda/2018b 5.3.0.post0 -Python-3.6.6 intel/2018b 6.0.x.post0 GCCcore/8.2.0 6.0.x.post0 GCCcore/8.3.0 7.1.2 GCCcore/10.2.0 7.1.2 -Python-3.8.2 GCCcore/9.3.0 8.2.0 GCCcore/10.3.0 8.3.1 GCCcore/11.2.0 8.3.2 GCCcore/11.2.0 9.2.0 GCCcore/11.3.0 9.5.0 GCCcore/12.2.0 9.5.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Pillow/","title":"Pillow","text":"Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
homepage: https://pillow.readthedocs.org/
version versionsuffix toolchain 10.0.0 GCCcore/12.3.0 10.2.0 GCCcore/13.2.0 10.4.0 GCCcore/13.3.0 3.2.0 -Python-2.7.11-freetype-2.6.3 foss/2016a 3.2.0 -Python-2.7.11-freetype-2.6.3 intel/2016a 3.2.0 -Python-2.7.11 intel/2016a 3.4.2 -Python-3.5.2 foss/2016b 3.4.2 -Python-2.7.12 intel/2016b 3.4.2 -Python-3.5.2-freetype-2.6.5 intel/2016b 3.4.2 -Python-3.5.2 intel/2016b 4.1.0 -Python-2.7.13 intel/2017a 4.1.1 -Python-3.6.1 intel/2017a 4.2.1 -Python-3.6.1 intel/2017a 4.3.0 -Python-3.6.3 foss/2017b 4.3.0 -Python-2.7.13 intel/2017a 4.3.0 -Python-2.7.14 intel/2017b 5.0.0 -Python-2.7.14 foss/2017b 5.0.0 -Python-3.6.3 foss/2017b 5.0.0 -Python-3.6.4 foss/2018a 5.0.0 -Python-2.7.14 intel/2017b 5.0.0 -Python-3.6.3 intel/2017b 5.0.0 -Python-2.7.14 intel/2018a 5.0.0 -Python-3.6.4 intel/2018a 5.3.0 -Python-2.7.15 foss/2018b 5.3.0 -Python-3.6.6 foss/2018b 5.3.0 -Python-3.6.6 fosscuda/2018b 5.3.0 -Python-3.6.6 intel/2018b 6.0.0 GCCcore/8.2.0 6.2.1 GCCcore/8.3.0 6.2.2 -Python-2.7.18 foss/2020b 7.0.0 -Python-3.8.2 GCCcore/9.3.0 8.0.1 GCCcore/10.2.0 8.2.0 GCCcore/10.3.0 8.3.1 GCCcore/11.2.0 8.3.2 GCCcore/11.2.0 9.1.0 GCCcore/10.3.0 9.1.1 GCCcore/11.2.0 9.1.1 GCCcore/11.3.0 9.2.0 GCCcore/10.2.0 9.4.0 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Pilon/","title":"Pilon","text":"Pilon is an automated genome assembly improvement and variant detection tool
homepage: https://github.com/broadinstitute/pilon
version versionsuffix toolchain 1.22 -Java-1.8.0_162 system 1.22 -Java-1.8 system 1.23 -Java-1.8 system 1.23 -Java-11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Pindel/","title":"Pindel","text":"Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
homepage: http://gmt.genome.wustl.edu/packages/pindel/
version toolchain 0.2.5b8 foss/2016b 0.2.5b9-20170508 GCC/11.2.0 0.2.5b9-20170508 GCC/11.3.0 0.2.5b9-20170508 GCC/6.4.0-2.28 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Pingouin/","title":"Pingouin","text":"Pingouin is an open-source statistical package written in Python 3 and based mostly on Pandas and NumPy.
homepage: https://pingouin-stats.org/
version versionsuffix toolchain 0.3.8 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Pint/","title":"Pint","text":"Pint is a Python package to define, operate and manipulate physical quantities: the product of a numerical value and a unit of measurement. It allows arithmetic operations between them and conversions from and to different units.
homepage: https://github.com/hgrecco/pint
version versionsuffix toolchain 0.14 -Python-3.7.4 GCCcore/8.3.0 0.19.2 GCCcore/11.2.0 0.20.1 GCCcore/10.3.0 0.22 GCCcore/11.3.0 0.23 GCCcore/12.3.0 0.24 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Pisces/","title":"Pisces","text":"Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
homepage: https://github.com/Illumina/Pisces
version toolchain 5.2.7.47 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PlaScope/","title":"PlaScope","text":"Plasmid exploration of bacterial genomes
homepage: https://github.com/GuilhemRoyer/PlaScope
version toolchain 1.3.1 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PlasmaPy/","title":"PlasmaPy","text":"Open source Python ecosystem for plasma research and education
homepage: https://www.plasmapy.org
version versionsuffix toolchain 0.3.1 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Platanus/","title":"Platanus","text":"PLATform for Assembling NUcleotide Sequences
homepage: http://platanus.bio.titech.ac.jp/
version versionsuffix toolchain 1.2.1 -linux-x86_64 system 1.2.4 foss/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Platypus-Opt/","title":"Platypus-Opt","text":"Platypus is a framework for evolutionary computing in Python with a focus on multiobjective evolutionary algorithms (MOEAs).
homepage: https://github.com/Project-Platypus/Platypus
version toolchain 1.1.0 foss/2022a 1.2.0 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Platypus/","title":"Platypus","text":"Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data.
homepage: http://www.well.ox.ac.uk/platypus
version versionsuffix toolchain 0.8.1 -Python-2.7.11 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Ploticus/","title":"Ploticus","text":"Ploticus is a free GPL software utility that can produce various types of plots and graphs
homepage: http://ploticus.sourceforge.net/doc/welcome.html
version toolchain 2.42 GCCcore/7.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PnetCDF/","title":"PnetCDF","text":"Parallel netCDF: A Parallel I/O Library for NetCDF File Access
homepage: https://parallel-netcdf.github.io/
version toolchain 1.10.0 foss/2018b 1.10.0 intel/2018b 1.12.1 gompi/2019b 1.12.1 gompi/2020a 1.12.1 gompic/2019b 1.12.1 gompic/2020a 1.12.1 iimpi/2020a 1.12.2 gompi/2020b 1.12.2 gompi/2021a 1.12.2 gompic/2020b 1.12.2 iimpi/2021a 1.12.3 gompi/2021b 1.12.3 gompi/2022a 1.12.3 gompi/2023a 1.12.3 iimpi/2022a 1.13.0 iimpi/2023a 1.8.1 intel/2017a 1.9.0 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Porechop/","title":"Porechop","text":"Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity
homepage: https://github.com/rrwick/Porechop
version versionsuffix toolchain 0.2.3 -Python-3.5.2 foss/2016b 0.2.4 GCCcore/10.3.0 0.2.4 GCCcore/11.2.0 0.2.4 -Python-3.6.6 foss/2018b 0.2.4 -Python-3.7.4 intel/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PortAudio/","title":"PortAudio","text":"PortAudio is a free, cross-platform, open-source, audio I/O library. It lets you write simple audio programs in 'C' or C++ that will compile and run on many platforms including Windows, Macintosh OS X, and Unix (OSS/ALSA). It is intended to promote the exchange of audio software between developers on different platforms. Many applications use PortAudio for Audio I/O.
homepage: https://www.portaudio.com/
version toolchain 19.7.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PortMidi/","title":"PortMidi","text":"PortMidi is a library for software developers. It supports real-time input and output of MIDI data using a system-independent interface. PortMidi runs on Windows (using MME), Macintosh (using CoreMIDI), and Linux (using ALSA).
homepage: https://github.com/PortMidi/portmidi
version toolchain 2.0.4 GCCcore/11.3.0 2.0.4 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Portcullis/","title":"Portcullis","text":"Portcullis stands for PORTable CULLing of Invalid Splice junctions from pre-aligned RNA-seq data. It is known that RNAseq mapping tools generate many invalid junction predictions, particularly in deep datasets with high coverage over splice sites. In order to address this, instead for creating a new RNAseq mapper, with a focus on SJ accuracy we created a tool that takes in a BAM file generated by an RNAseq mapper of the user's own choice (e.g. Tophat2, Gsnap, STAR2 or HISAT2) as input (i.e. it's portable). It then, analyses and quantifies all splice junctions in the file before, filtering (culling) those which are unlikely to be genuine. Portcullis output's junctions in a variety of formats making it suitable for downstream analysis (such as differential splicing analysis and gene modelling) without additional work. Portcullis can also filter the original BAM file removing alignments associated with bad junctions.
homepage: https://github.com/maplesond/portcullis
version versionsuffix toolchain 1.2.2 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PostgreSQL/","title":"PostgreSQL","text":"PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.
homepage: https://www.postgresql.org/
version versionsuffix toolchain 10.2 -Python-2.7.14 intel/2018a 10.3 -Python-2.7.14 foss/2017b 10.3 -Python-2.7.14 foss/2018a 10.3 foss/2018b 10.3 -Python-2.7.14 intel/2017b 10.3 -Python-2.7.14 intel/2018a 11.3 -Python-2.7.15 GCCcore/8.2.0 11.3 -Python-3.7.2 GCCcore/8.2.0 12.4 GCCcore/9.3.0 13.2 GCCcore/10.2.0 13.3 GCCcore/10.3.0 13.4 GCCcore/11.2.0 14.4 GCCcore/11.3.0 15.2 GCCcore/12.2.0 16.1 GCCcore/12.3.0 16.1 GCCcore/13.2.0 16.4 GCCcore/13.3.0 9.4.7 -Python-2.7.11 intel/2016a 9.5.2 -Python-2.7.11 intel/2016a 9.6.0 -Python-2.7.12 intel/2016b 9.6.2 -Python-2.7.12 foss/2016b 9.6.2 -Python-2.7.12 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Postgres-XL/","title":"Postgres-XL","text":"Postgres-XL is a horizontally scalable open source SQL database cluster, flexible enough to handle varying database workloads:
homepage: http://www.postgres-xl.org
version versionsuffix toolchain 9.5r1 -Python-2.7.11 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PretextMap/","title":"PretextMap","text":"Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.
homepage: https://github.com/sanger-tol/PretextMap/
version toolchain 0.1.9 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Primer3/","title":"Primer3","text":"Primer3 is a widely used program for designing PCR primers (PCR = 'Polymerase Chain Reaction'). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.
homepage: http://primer3.sourceforge.net
version toolchain 2.3.7 intel/2017b 2.4.0 iccifort/2019.1.144-GCC-8.2.0-2.31.1 2.4.0 intel/2018b 2.5.0 GCC/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/ProBiS/","title":"ProBiS","text":"ProBiS algorithm aligns and superimposes complete protein surfaces, surface motifs, or protein binding sites.
homepage: http://insilab.org/probis-algorithm
version toolchain 20230403 gompi/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/ProFit/","title":"ProFit","text":"ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate program for performing least squares fits of two or more protein structures. It performs a very simple and basic function, but allows as much flexibility as possible in performing this procedure. Thus one can specify subsets of atoms to be considered, specify zones to be fitted by number, sequence, or by sequence alignment.
homepage: http://www.bioinf.org.uk/software/profit
version toolchain 3.3 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/ProbABEL/","title":"ProbABEL","text":"Tool for genome-wide association analysis of imputed genetic data.
homepage: https://github.com/GenABEL-Project/ProbABEL
version toolchain 0.5.0 GCCcore/9.3.0 0.5.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/ProjectQ/","title":"ProjectQ","text":"An open source software framework for quantum computing
homepage: https://projectq.ch
version versionsuffix toolchain 0.4.2 -Python-3.6.6 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/ProtHint/","title":"ProtHint","text":"ProtHint is a pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences.
homepage: https://github.com/gatech-genemark/ProtHint
version versionsuffix toolchain 2.4.0 -Python-3.7.2 iccifort/2019.1.144-GCC-8.2.0-2.31.1 2.4.0 -Python-3.7.4 iccifort/2019.5.281 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/ProteinMPNN/","title":"ProteinMPNN","text":"A deep learning based protein sequence design method is described that is widely applicable to current design challenges and shows outstanding performance in both in silico and experimental tests.
homepage: https://github.com/dauparas/ProteinMPNN
version versionsuffix toolchain 1.0.1-20230627 -CUDA-11.7.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/Proteinortho/","title":"Proteinortho","text":"Proteinortho is a tool to detect orthologous genes within different species.
homepage: http://www.bioinf.uni-leipzig.de/Software/proteinortho/
version versionsuffix toolchain 5.16b -Python-3.6.4-Perl-5.26.1 foss/2018a 6.2.3 gompi/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PsiCLASS/","title":"PsiCLASS","text":"PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.
homepage: https://github.com/splicebox/PsiCLASS
version toolchain 1.0.3 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PuLP/","title":"PuLP","text":"PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to solve linear problems.
homepage: https://github.com/coin-or/pulp
version toolchain 2.5.1 foss/2021a 2.7.0 foss/2022b 2.8.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PyAEDT/","title":"PyAEDT","text":"PyAEDT is a Python library that interacts directly with the Ansys Electronics Desktop (AEDT) API, enabling straightforward and efficient automation in your workflow.
homepage: https://aedt.docs.pyansys.com/version/stable
version toolchain 0.8.7 GCCcore/12.3.0 0.9.9 gfbf/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PyAMG/","title":"PyAMG","text":"PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface.
homepage: http://pyamg.org
version versionsuffix toolchain 3.0.1 -Python-2.7.11 intel/2016a 4.0.0 foss/2020b 4.0.0 intel/2020b 4.2.3 foss/2021a 5.1.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PyAPS3/","title":"PyAPS3","text":"Python 3 Atmospheric Phase Screen
homepage: https://github.com/AngeliqueBenoit/pyaps3
version versionsuffix toolchain 20190407 -Python-3.7.2 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PyAV/","title":"PyAV","text":"PyAV is a Pythonic binding for FFmpeg. We aim to provide all of the power and control of the underlying library, but manage the gritty details as much as possible.
homepage: https://pyav.org
version toolchain 10.0.0 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PyBEL/","title":"PyBEL","text":"PyBEL is a pure Python software package that parses BEL (Biological Expression Language) documents, validates their semantics, and facilitates data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J.
homepage: https://github.com/pybel/pybel
version toolchain 0.15.5 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/PyBerny/","title":"PyBerny","text":"PyBerny is an optimizer of molecular geometries with respect to the total energy, using nuclear gradient information.
homepage: https://github.com/jhrmnn/pyberny
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version toolchain 3.10.4 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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","boost":0.5},{"location":"version-specific/supported-software/p/parallel-fastq-dump/","title":"parallel-fastq-dump","text":"parallel fastq-dump wrapper
homepage: https://github.com/rvalieris/parallel-fastq-dump
version versionsuffix toolchain 0.6.5 -Python-3.7.2 GCCcore/8.2.0 0.6.6 -Python-3.8.2 GCCcore/9.3.0 0.6.7 gompi/2020b 0.6.7 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/parallel/","title":"parallel","text":"parallel: Build and execute shell commands in parallel
homepage: http://savannah.gnu.org/projects/parallel/
version toolchain 20141122 GCC/4.9.2 20150322 GCC/4.9.2 20150822 GCC/4.9.2 20160622 foss/2016a 20170822 intel/2017a 20171022 intel/2017b 20171122 foss/2017b 20171122 intel/2017b 20180422 intel/2018a 20180822 foss/2018b 20181222 intel/2018b 20190222 GCCcore/7.3.0 20190622 GCCcore/8.2.0 20190922 GCCcore/8.3.0 20200422 GCCcore/9.3.0 20200522 GCCcore/9.3.0 20210322 GCCcore/10.2.0 20210622 GCCcore/10.3.0 20210722 GCCcore/11.2.0 20220722 GCCcore/11.3.0 20230722 GCCcore/12.2.0 20230722 GCCcore/12.3.0 20240322 GCCcore/13.2.0 20240722 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/parameterized/","title":"parameterized","text":"Parameterized testing with any Python test framework
homepage: https://github.com/wolever/parameterized
version toolchain 0.8.1 GCCcore/10.3.0 0.9.0 GCCcore/11.3.0 0.9.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/paramiko/","title":"paramiko","text":"Paramiko is a pure-Python (3.6+) implementation of the SSHv2 protocol, providing both client and server functionality. It provides the foundation for the high-level SSH library Fabric, which is what we recommend you use for common client use-cases such as running remote shell commands or transferring files.
homepage: https://paramiko.org
version toolchain 3.2.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/parasail/","title":"parasail","text":"parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms.
homepage: https://github.com/jeffdaily/parasail
version toolchain 2.2 intel/2018a 2.4 foss/2018b 2.4.1 GCC/8.3.0 2.4.1 intel/2019b 2.4.2 GCC/9.3.0 2.4.2 iccifort/2020.1.217 2.4.3 GCC/10.2.0 2.4.3 GCC/10.3.0 2.5 GCC/11.2.0 2.6 GCC/11.3.0 2.6.2 GCC/12.2.0 2.6.2 GCC/12.3.0 2.6.2 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pasta/","title":"pasta","text":"PASTA (Practical Alignment using SATe and Transitivity)
homepage: https://github.com/smirarab/pasta
version versionsuffix toolchain 1.8.5 -Python-3.7.2 GCC/8.2.0-2.31.1 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pastml/","title":"pastml","text":"Ancestor character reconstruction and visualisation for rooted phylogenetic trees
homepage: https://pastml.pasteur.fr/
version toolchain 1.9.34 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/patch/","title":"patch","text":"Patch takes a patch file containing a difference listing produced by the diff program and applies those differences to one or more original files, producing patched versions.
homepage: https://savannah.gnu.org/projects/patch
version toolchain 2.7.6 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/patchelf/","title":"patchelf","text":"PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.
homepage: http://nixos.org/patchelf.html
version toolchain 0.10 GCCcore/7.2.0 0.10 GCCcore/8.3.0 0.12 GCCcore/10.2.0 0.12 GCCcore/10.3.0 0.12 GCCcore/9.3.0 0.13 GCCcore/11.2.0 0.15.0 GCCcore/11.3.0 0.17.2 GCCcore/12.2.0 0.18.0 GCCcore/12.3.0 0.18.0 GCCcore/13.2.0 0.18.0 GCCcore/13.3.0 0.8 GNU/4.9.3-2.25 0.9 GCCcore/6.4.0 0.9 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/path.py/","title":"path.py","text":"path.py is a Python library implementing path objects as first-class entities, allowing common operations on files to be invoked on those path objects directly.
homepage: https://github.com/jaraco/path.py
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","boost":0.5},{"location":"version-specific/supported-software/p/pauvre/","title":"pauvre","text":"Tools for plotting Oxford Nanopore and other long-read data
homepage: https://github.com/conchoecia/pauvre
version versionsuffix toolchain 0.1923 -Python-3.7.4 intel/2019b 0.1924 intel/2020b 0.2.3 foss/2021a 0.2.3 foss/2022a 0.2.3 foss/2022b 0.2.3 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pbbam/","title":"pbbam","text":"The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices.
homepage: http://pbbam.readthedocs.io/
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","boost":0.5},{"location":"version-specific/supported-software/p/pbcopper/","title":"pbcopper","text":"The pbcopper library provides a suite of data structures, algorithms, and utilities for C++ applications.
homepage: https://github.com/PacificBiosciences/pbcopper
version toolchain 1.3.0 gompi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pbdagcon/","title":"pbdagcon","text":"pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus) which is a sequence consensus algorithm based on using directed acyclic graphs to encode multiple sequence alignment.
homepage: https://github.com/PacificBiosciences/pbdagcon
version toolchain 20170330 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pbipa/","title":"pbipa","text":"Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies. IPA is an end-to-end solution, starting with input reads and resulting in a polished assembly. IPA is fast, providing an easy to use local run mode or a distributed pipeline for a cluster.
homepage: https://github.com/PacificBiosciences/pbipa
version toolchain 1.8.0 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pblat/","title":"pblat","text":"When the query file format is fasta, you can specify many threads to process it. It can reduce run time linearly, and use almost equal memory as the original blat program. This is useful when you blat a big query file to a huge reference like human whole genome sequence.
homepage: https://github.com/icebert/pblat
version toolchain 2.5.1 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pbmm2/","title":"pbmm2","text":"A minimap2 frontend for PacBio native data formats
homepage: https://github.com/PacificBiosciences/pbmm2
version toolchain 1.1.0 gompi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pbs_python/","title":"pbs_python","text":"The pbs_python package is a wrapper class for the Torque C library. With this package you now can write utilities/extensions in Python instead of C. We developed this package because we want to replace xpbsmon by an ascii version named pbsmon. PBSQuery is also included in this package. This is a python module build on top of the pbs python module to simplify querying the batch server, eg: how many jobs, how many nodes, ...
homepage: https://oss.trac.surfsara.nl/pbs_python
version versionsuffix toolchain 4.6.0 -Python-2.7.11 intel/2016a 4.6.0 -Python-2.7.12 intel/2016b 4.6.0 -Python-2.7.13 intel/2017a 4.6.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pdf2docx/","title":"pdf2docx","text":"Open source Python library converting pdf to docx.
homepage: https://github.com/ArtifexSoftware/pdf2docx
version toolchain 0.5.8 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pdsh/","title":"pdsh","text":"A high performance, parallel remote shell utility
homepage: https://github.com/chaos/pdsh
version toolchain 2.34 GCCcore/11.3.0 2.34 GCCcore/12.2.0 2.34 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/peakdetect/","title":"peakdetect","text":"Simple peak detection library for Python based on Billauer's work and this gist.
homepage: https://github.com/avhn/peakdetect
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","boost":0.5},{"location":"version-specific/supported-software/p/perl-app-cpanminus/","title":"perl-app-cpanminus","text":"cpanm - get, unpack build and install modules from CPAN
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","boost":0.5},{"location":"version-specific/supported-software/p/petsc4py/","title":"petsc4py","text":"petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation.
homepage: https://bitbucket.org/petsc/petsc4py
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","boost":0.5},{"location":"version-specific/supported-software/p/pfind/","title":"pfind","text":"Drop-in replacement for find, implemented for using parallel access and MPI.
homepage: https://github.com/VI4IO/pfind
version toolchain 20220613 gompi/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pftoolsV3/","title":"pftoolsV3","text":"The pftools package contains all the software necessary to build protein and DNA generalized profiles and use them to scan and align sequences, and search databases.
homepage: http://web.expasy.org/pftools/
version toolchain 20160324 foss/2016a 3.2.11 GCCcore/10.3.0 3.2.11 foss/2021a 3.2.12 GCCcore/11.2.0 3.2.12 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/phasius/","title":"phasius","text":"A tool to visualize phase block structure from (many) BAM, CRAM or VCF files together with BED annotation
homepage: https://github.com/wdecoster/phasius
version toolchain 0.2.0 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/phonemizer/","title":"phonemizer","text":"The phonemizer allows simple phonemization of words and texts in many languages. Provides both the phonemize command-line tool and the Python function phonemizer.phonemize. It is using four backends: espeak, espeak-mbrola, festival and segments.
homepage: https://github.com/bootphon/phonemizer
version versionsuffix toolchain 2.2.1 -Python-3.8.2 gompi/2020a 3.2.1 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/phono3py/","title":"phono3py","text":"phono3py calculates phonon-phonon interaction and related properties using the supercell approach.
homepage: https://atztogo.github.io/phono3py/
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","boost":0.5},{"location":"version-specific/supported-software/p/phonopy/","title":"phonopy","text":"Phonopy is an open source package of phonon calculations based on the supercell approach.
homepage: https://atztogo.github.io/phonopy/
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","boost":0.5},{"location":"version-specific/supported-software/p/photontorch/","title":"photontorch","text":"Photontorch is a photonic simulator for highly parallel simulation and optimization of photonic circuits in time and frequency domain. Photontorch features CUDA enabled simulation and optimization of photonic circuits. It leverages the deep learning framework PyTorch to view the photonic circuit as essentially a recurrent neural network. This enables the use of native PyTorch optimizers to optimize the (physical) parameters of the circuit.
homepage: https://docs.photontorch.com/
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","boost":0.5},{"location":"version-specific/supported-software/p/phototonic/","title":"phototonic","text":"Phototonic is an image viewer and organizer
homepage: https://github.com/oferkv/phototonic
version toolchain 2.1 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/phylokit/","title":"phylokit","text":"C++ library for high performance phylogenetics
homepage: https://github.com/pranjalv123/phylokit
version toolchain 1.0 GCC/8.2.0-2.31.1 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/phylonaut/","title":"phylonaut","text":"Dynamic programming for phylogenetics applications
homepage: https://github.com/pranjalv123/phylonaut
version toolchain 20190626 gompi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/phyluce/","title":"phyluce","text":"phyluce is a software package for working with data generated from sequence capture of UCE (ultra-conserved element) loci, as first published in [BCF2012]. Specifically, phyluce is a suite of programs to: 1) assemble raw sequence reads from Illumina platforms into contigs 2) determine which contigs represent UCE loci 3) filter potentially paralagous UCE loci 4) generate different sets of UCE loci across taxa of interest
homepage: https://github.com/faircloth-lab/phyluce
version toolchain 1.7.3 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/phyx/","title":"phyx","text":"phyx performs phylogenetics analyses on trees and sequences.
homepage: https://github.com/FePhyFoFum/phyx
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","boost":0.5},{"location":"version-specific/supported-software/p/piSvM-JSC/","title":"piSvM-JSC","text":"piSvM is a parallel implementation of the Support Vector Machine (SVM) algorithm that allows efficient training and testing on a multiprocessor system. This version is a fork of the original PiSvM to increase scalability.
homepage: https://github.com/mricherzhagen/pisvm
version toolchain 1.2-20150622 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/piSvM/","title":"piSvM","text":"piSvM is a parallel implementation of the Support Vector Machine (SVM) algorithm that allows efficient training and testing on a multiprocessor system.
homepage: http://pisvm.sourceforge.net/
version toolchain 1.3 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/picard/","title":"picard","text":"A set of tools (in Java) for working with next generation sequencing data in the BAM format.
homepage: http://sourceforge.net/projects/picard
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","boost":0.5},{"location":"version-specific/supported-software/p/pigz/","title":"pigz","text":"pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries.
homepage: http://zlib.net/pigz/
version toolchain 2.3.3 foss/2016b 2.3.4 GCCcore/6.4.0 2.4 GCCcore/10.2.0 2.4 GCCcore/6.4.0 2.4 GCCcore/7.3.0 2.4 GCCcore/8.2.0 2.4 GCCcore/8.3.0 2.4 GCCcore/9.3.0 2.4 foss/2018a 2.6 GCCcore/10.2.0 2.6 GCCcore/10.3.0 2.6 GCCcore/11.2.0 2.7 GCCcore/11.3.0 2.7 GCCcore/12.2.0 2.8 GCCcore/12.3.0 2.8 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pip/","title":"pip","text":"The PyPA recommended tool for installing Python packages.
homepage: https://pip.pypa.io
version versionsuffix toolchain 8.0.2 -Python-2.7.11 intel/2016a 8.1.2 -Python-2.7.11 foss/2016a 8.1.2 -Python-2.7.12 foss/2016b 8.1.2 -Python-2.7.12 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pixman/","title":"pixman","text":"Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.
homepage: http://www.pixman.org/
version toolchain 0.34.0 GCCcore/5.4.0 0.34.0 GCCcore/6.3.0 0.34.0 GCCcore/6.4.0 0.34.0 GCCcore/7.3.0 0.34.0 foss/2016a 0.34.0 foss/2016b 0.34.0 intel/2016a 0.34.0 intel/2016b 0.38.0 GCCcore/8.2.0 0.38.4 GCCcore/8.3.0 0.38.4 GCCcore/9.3.0 0.40.0 GCCcore/10.2.0 0.40.0 GCCcore/10.3.0 0.40.0 GCCcore/11.2.0 0.40.0 GCCcore/11.3.0 0.42.2 GCCcore/12.2.0 0.42.2 GCCcore/12.3.0 0.42.2 GCCcore/13.2.0 0.43.4 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pizzly/","title":"pizzly","text":"Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.
homepage: https://github.com/pmelsted/pizzly
version toolchain 0.37.3 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pkg-config/","title":"pkg-config","text":"pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c pkg-config --libs --cflags glib-2.0 for instance, rather than hard-coding values on where to find glib (or other libraries).
homepage: http://www.freedesktop.org/wiki/Software/pkg-config/
version toolchain 0.28 GCC/4.8.2 0.28 GCC/4.9.2 0.28 GNU/4.9.3-2.25 0.29 foss/2016a 0.29 gimkl/2.11.5 0.29 intel/2016a 0.29.1 GCCcore/4.9.3 0.29.1 GCCcore/5.4.0 0.29.1 GCCcore/6.3.0 0.29.1 foss/2016a 0.29.1 foss/2016b 0.29.1 foss/2017a 0.29.1 gimkl/2017a 0.29.1 intel/2016a 0.29.1 intel/2016b 0.29.1 intel/2017a 0.29.2 GCCcore/10.2.0 0.29.2 GCCcore/10.3.0 0.29.2 GCCcore/11.2.0 0.29.2 GCCcore/11.3.0 0.29.2 GCCcore/12.2.0 0.29.2 GCCcore/6.3.0 0.29.2 GCCcore/6.4.0 0.29.2 GCCcore/7.2.0 0.29.2 GCCcore/7.3.0 0.29.2 GCCcore/8.2.0 0.29.2 GCCcore/8.3.0 0.29.2 GCCcore/9.3.0 0.29.2 intel/2017a 0.29.2 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pkgconf/","title":"pkgconf","text":"pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org.
homepage: https://github.com/pkgconf/pkgconf
version toolchain 1.8.0 GCCcore/10.3.0 1.8.0 GCCcore/11.2.0 1.8.0 GCCcore/11.3.0 1.8.0 system 1.9.3 GCCcore/12.2.0 1.9.4 GCCcore/13.1.0 1.9.5 GCCcore/12.3.0 2.0.3 GCCcore/13.2.0 2.2.0 GCCcore/13.3.0 2.2.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pkgconfig/","title":"pkgconfig","text":"pkgconfig is a Python module to interface with the pkg-config command line tool
homepage: https://github.com/matze/pkgconfig
version versionsuffix toolchain 1.1.0 -Python-2.7.11 foss/2016a 1.1.0 -Python-3.5.1 foss/2016a 1.1.0 -Python-2.7.12 foss/2016b 1.1.0 -Python-3.5.2 foss/2016b 1.1.0 -Python-2.7.11 intel/2016a 1.1.0 -Python-2.7.12 intel/2016b 1.1.0 -Python-3.5.2 intel/2016b 1.2.2 -Python-2.7.13 foss/2017a 1.2.2 -Python-3.6.1 foss/2017a 1.2.2 -Python-2.7.14 foss/2017b 1.2.2 -Python-3.6.3 foss/2017b 1.2.2 -Python-2.7.14 fosscuda/2017b 1.2.2 -Python-3.6.3 fosscuda/2017b 1.2.2 -Python-2.7.13 intel/2017a 1.2.2 -Python-3.6.1 intel/2017a 1.2.2 -Python-2.7.14 intel/2017b 1.2.2 -Python-3.6.3 intel/2017b 1.3.1 -Python-2.7.14 foss/2018a 1.3.1 -Python-3.6.4 foss/2018a 1.3.1 -Python-2.7.15 foss/2018b 1.3.1 -Python-3.6.6 foss/2018b 1.3.1 -Python-2.7.15 fosscuda/2018b 1.3.1 -Python-3.6.6 fosscuda/2018b 1.3.1 -Python-2.7.14 intel/2018a 1.3.1 -Python-3.6.4 intel/2018a 1.3.1 -Python-2.7.15 intel/2018b 1.3.1 -Python-3.6.6 intel/2018b 1.5.1 -python GCCcore/10.2.0 1.5.1 -python GCCcore/8.2.0 1.5.1 -Python-3.7.4 GCCcore/8.3.0 1.5.1 -Python-3.8.2 GCCcore/9.3.0 1.5.4 -python GCCcore/10.3.0 1.5.5 -python GCCcore/11.2.0 1.5.5 -python GCCcore/11.3.0 1.5.5 -python GCCcore/12.2.0 1.5.5 -python GCCcore/12.3.0 1.5.5 -python GCCcore/13.2.0 1.5.5 -python GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/planarity/","title":"planarity","text":"A library for implementing graph algorithms
homepage: https://github.com/graph-algorithms/edge-addition-planarity-suite
version toolchain 3.0.2.0 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/plantcv/","title":"plantcv","text":"PlantCV: Plant phenotyping using computer vision.
homepage: https://pypi.org/project/plantcv/
version versionsuffix toolchain 3.8.0 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/plantri/","title":"plantri","text":"Plantri is a program that generates certain types of graphs that are imbedded on the sphere. Exactly one member of each isomorphism class is output, using an amount of memory almost independent of the number of graphs produced. This, together with the exceptionally fast operation and careful validation, makes the program suitable for processing very large numbers of graphs. Isomorphisms are defined with respect to the embeddings, so in some cases outputs may be isomorphic as abstract graphs.
homepage: https://doc.sagemath.org/html/en/reference/spkg/plantri.html
version toolchain 5.4 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/plc/","title":"plc","text":"plc is the public Planck Likelihood Code. It provides C and Fortran libraries that allow users to compute the log likelihoods of the temperature, polarization, and lensing maps. Optionally, it also provides a python version of this library, as well as tools to modify the predetermined options for some likelihoods (e.g. changing the high-ell and low-ell lmin and lmax values of the temperature).
homepage: http://pla.esac.esa.int/pla/#home
version versionsuffix toolchain 3.0.1 -Python-2.7.15 foss/2019a 3.0.1 -Python-3.7.4 foss/2019b 3.0.1 -Python-2.7.15 intel/2018b 3.10 intel/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/plinkQC/","title":"plinkQC","text":"plinkQC is a R/CRAN package for genotype quality control in genetic association studies. It makes PLINK basic statistics (e.g.missing genotyping rates per individual, allele frequencies per genetic marker) and relationship functions easily accessible from within R and allows for automatic evaluation of the results.
homepage: https://meyer-lab-cshl.github.io/plinkQC/
version versionsuffix toolchain 0.3.3 -R-4.0.0 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/plinkliftover/","title":"plinkliftover","text":"PLINKLiftOver is a utility enabling liftOver to work on genomics files from PLINK, allowing one to update the coordinates from one genome reference version to another.
homepage: https://github.com/milescsmith/plinkliftover
version toolchain 0.3.0 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/plmc/","title":"plmc","text":"Inference of couplings in proteins and RNAs from sequence variation.
homepage: https://github.com/debbiemarkslab/plmc
version versionsuffix toolchain 20230121 -32bit GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/plot1cell/","title":"plot1cell","text":"plot1cell: a package for advanced single cell data visualization
homepage: https://github.com/HaojiaWu/plot1cell
version versionsuffix toolchain 0.0.1 -R-4.2.1 foss/2022a 0.0.1 -R-4.2.2 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/plotly-orca/","title":"plotly-orca","text":"Orca is an Electron app that generates images and reports of Plotly things like plotly.js graphs, dash apps, dashboards from the command line.
homepage: https://github.com/plotly/orca
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","boost":0.5},{"location":"version-specific/supported-software/p/plotly/","title":"plotly","text":"Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R.
homepage: https://cran.r-project.org/web/packages/plotly
version versionsuffix toolchain 4.7.1 -R-3.4.0 intel/2017a 4.8.0 -R-3.4.4 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/plotly.py/","title":"plotly.py","text":"An open-source, interactive graphing library for Python
homepage: https://plot.ly/python
version toolchain 4.1.0 intel/2019a 4.14.3 GCCcore/10.2.0 4.14.3 GCCcore/10.3.0 4.4.1 intel/2019b 4.8.1 GCCcore/9.3.0 5.1.0 GCCcore/10.3.0 5.12.0 GCCcore/11.3.0 5.13.1 GCCcore/12.2.0 5.16.0 GCCcore/12.3.0 5.18.0 GCCcore/13.2.0 5.4.0 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/plotutils/","title":"plotutils","text":"The GNU plotutils package contains software for both programmers and technical users. Its centerpiece is libplot, a powerful C/C++ function library for exporting 2-D vector graphics in many file formats, both vector and bitmap. On the X Window System, it can also do 2-D vector graphics animations. libplot is device-independent, in the sense that its API (application programming interface) does not depend on the type of graphics file to be exported. A Postscript-like API is used both for file export and for graphics animations. A libplot programmer needs to learn only one API: not the details of many graphics file formats.
homepage: https://www.gnu.org/software/plotutils/
version toolchain 2.6 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pmt/","title":"pmt","text":"PMT is a high-level software library capable of collecting power consumption measurements on various hardware.
homepage: https://git.astron.nl/RD/pmt
version versionsuffix toolchain 1.1.0 GCCcore/11.3.0 1.2.0 -CUDA-11.7.0 GCCcore/11.3.0 1.2.0 GCCcore/11.3.0 1.2.0 -CUDA-12.1.1 GCCcore/12.3.0 1.2.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pmx/","title":"pmx","text":"pmx (formerly pymacs) is a small bunch of classes to read structure files such as pdb or gro and trajectory data in gromacs xtc format. Over the years it has been extended towards a versatile (bio-) molecular structure manipulation package with some additional functionalities, e.g. gromacs file parsers and scripts for setup and analysis of free energy calculations.
homepage: https://github.com/deGrootLab/pmx
version versionsuffix toolchain 2.0 -Python-2.7.18 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pocl/","title":"pocl","text":"Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard
homepage: http://portablecl.org
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","boost":0.5},{"location":"version-specific/supported-software/p/pod5-file-format/","title":"pod5-file-format","text":"POD5 is a file format for storing nanopore dna data in an easily accessible way. The format is able to be written in a streaming manner which allows a sequencing instrument to directly write the format.
homepage: https://github.com/nanoporetech/pod5-file-format
version toolchain 0.1.8 foss/2022a 0.3.10 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/poetry/","title":"poetry","text":"Python packaging and dependency management made easy
homepage: https://python-poetry.org/
version versionsuffix toolchain 1.0.9 -Python-3.8.2 GCCcore/9.3.0 1.2.2 GCCcore/11.3.0 1.5.1 GCCcore/12.3.0 1.6.1 GCCcore/13.2.0 1.7.1 GCCcore/12.3.0 1.8.3 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/polars/","title":"polars","text":"Lightning-fast DataFrame library for Rust and Python.
homepage: https://pola.rs/
version toolchain 0.15.6 foss/2022a 0.20.2 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/polymake/","title":"polymake","text":"polymake is open source software for research in polyhedral geometry. It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, graphs, tropical hypersurfaces, and other objects.
homepage: https://polymake.org
version toolchain 4.0r1 foss/2019b 4.8 foss/2021b 4.8 gfbf/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pomkl/","title":"pomkl","text":"Toolchain with PGI C, C++ and Fortran compilers, alongside Intel MKL & OpenMPI.
homepage: http://www.pgroup.com/index.htm
version toolchain 2016.03 system 2016.04 system 2016.09 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pompi/","title":"pompi","text":"Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI.
homepage: http://www.pgroup.com/index.htm
version toolchain 2016.03 system 2016.04 system 2016.09 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/poppler/","title":"poppler","text":"Poppler is a PDF rendering library based on the xpdf-3.0 code base.
homepage: https://poppler.freedesktop.org/
version toolchain 0.70.1 foss/2018b 0.90.1 GCCcore/8.3.0 21.06.1 GCC/10.2.0 21.06.1 GCC/10.3.0 22.01.0 GCC/11.2.0 22.12.0 GCC/11.3.0 23.09.0 GCC/12.3.0 24.04.0 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/poppunk/","title":"poppunk","text":"PopPUNK is a tool for clustering genomes. We refer to the clusters as variable-length-k-mer clusters, or VLKCs. Biologically, these clusters typically represent distinct strains. We refer to subclusters of strains as lineages.
homepage: https://poppunk.readthedocs.io
version toolchain 2.6.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/popscle/","title":"popscle","text":"A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools
homepage: https://github.com/statgen/popscle
version toolchain 0.1-beta-20210505 GCC/11.3.0 0.1-beta foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/popt/","title":"popt","text":"Popt is a C library for parsing command line parameters.
homepage: http://freecode.com/projects/popt
version toolchain 1.14 GCC/4.8.2 1.16 GCC/10.2.0 1.16 GCC/4.9.2 1.16 system 1.19 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/porefoam/","title":"porefoam","text":"Direct pore-scale simulation of single- and two-phase flow through confined media
homepage: https://github.com/ImperialCollegeLondon/porefoam
version toolchain 2021-09-21 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/poretools/","title":"poretools","text":"A toolkit for working with nanopore sequencing data from Oxford Nanopore.
homepage: https://poretools.readthedocs.io/en/latest/
version versionsuffix toolchain 0.6.0 -Python-2.7.14 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/powerlaw/","title":"powerlaw","text":"powerlaw: A Python Package for Analysis of Heavy-Tailed Distributions
homepage: http://www.github.com/jeffalstott/powerlaw
version toolchain 1.5 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pp-sketchlib/","title":"pp-sketchlib","text":"Library of sketching functions used by PopPUNK
homepage: https://github.com/bacpop/pp-sketchlib
version toolchain 2.1.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/ppl/","title":"ppl","text":"The Parma Polyhedra Library (PPL) provides numerical abstractions especially targeted at applications in the field of analysis and verification of complex systems.
homepage: https://www.bugseng.com/parma-polyhedra-library
version toolchain 1.2 GCCcore/11.3.0 1.2 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/pplacer/","title":"pplacer","text":"Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
homepage: http://matsen.fhcrc.org/pplacer/
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","boost":0.5},{"location":"version-specific/supported-software/p/pplpy/","title":"pplpy","text":"This Python package provides a wrapper to the C++ Parma Polyhedra Library (PPL).
homepage: https://pypi.org/project/pplpy/
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","boost":0.5},{"location":"version-specific/supported-software/p/preCICE/","title":"preCICE","text":"preCICE (Precise Code Interaction Coupling Environment) is a coupling library for partitioned multi-physics simulations, including, but not restricted to fluid-structure interaction and conjugate heat transfer simulations. Partitioned means that preCICE couples existing programs (solvers) capable of simulating a subpart of the complete physics involved in a simulation. This allows for the high flexibility that is needed to keep a decent time-to-solution for complex multi-physics scenarios.
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","boost":0.5},{"location":"version-specific/supported-software/p/premailer/","title":"premailer","text":"CSS blocks into inline style attributes for HTML emails
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version toolchain 3.10.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/preseq/","title":"preseq","text":"Software for predicting library complexity and genome coverage in high-throughput sequencing.
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","boost":0.5},{"location":"version-specific/supported-software/p/presto/","title":"presto","text":"Presto performs a fast Wilcoxon rank sum test and auROC analysis.
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","boost":0.5},{"location":"version-specific/supported-software/p/primecount/","title":"primecount","text":"primecount is a command-line program and C/C++ library that counts the number of primes \u2264 x (maximum 1031) using highly optimized implementations of the combinatorial prime counting algorithms.
homepage: https://github.com/kimwalisch/primecount
version toolchain 7.14 GCCcore/13.2.0 7.9 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/primecountpy/","title":"primecountpy","text":"This is a Cython interface to the C++ library primecount.
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version toolchain 0.1.0 GCCcore/11.3.0 0.1.0 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/printproto/","title":"printproto","text":"X.org PrintProto protocol headers.
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version toolchain 1.0.5 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: http://prodigal.ornl.gov/
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","boost":0.5},{"location":"version-specific/supported-software/p/prokka/","title":"prokka","text":"Prokka is a software tool for the rapid annotation of prokaryotic genomes.
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","boost":0.5},{"location":"version-specific/supported-software/p/prompt-toolkit/","title":"prompt-toolkit","text":"prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.
homepage: https://github.com/jonathanslenders/python-prompt-toolkit
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","boost":0.5},{"location":"version-specific/supported-software/p/proovread/","title":"proovread","text":"PacBio hybrid error correction through iterative short read consensus
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","boost":0.5},{"location":"version-specific/supported-software/p/propy/","title":"propy","text":"Propy is a protein description software. It allows analyzing sequence-derived structural and physicochemical features, which are very useful in representing and distinguishing proteins or peptides of different structural, functional and interaction properties. These have been widely used in developing methods and software for predicting protein structural and functional classes, protein-protein interactions, drug-target interactions, protein substrates, among others.
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","boost":0.5},{"location":"version-specific/supported-software/p/protobuf/","title":"protobuf","text":"Google Protocol Buffers
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","boost":0.5},{"location":"version-specific/supported-software/p/pscom/","title":"pscom","text":"ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer.
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homepage: https://github.com/lh3/psmc
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","boost":0.5},{"location":"version-specific/supported-software/p/psmpi/","title":"psmpi","text":"ParaStation MPI is an open source high-performance MPI 3.0 implementation, based on MPICH v3. It provides extra low level communication libraries and integration with various batch systems for tighter process control.
homepage: https://github.com/ParaStation/psmpi2
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","boost":0.5},{"location":"version-specific/supported-software/p/psycopg2/","title":"psycopg2","text":"Psycopg is the most popular PostgreSQL adapter for the Python programming language.
homepage: http://initd.org/psycopg/
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","boost":0.5},{"location":"version-specific/supported-software/p/ptemcee/","title":"ptemcee","text":"ptemcee, pronounced \"tem-cee\", is fork of Daniel Foreman-Mackey's wonderful emcee to implement parallel tempering more robustly. If you're trying to characterise awkward, multi-model probability distributions, then ptemcee is your friend.
homepage: https://github.com/willvousden/ptemcee
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homepage: https://github.com/phbradley/pubtcrs
version toolchain 20180622 intel/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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","boost":0.5},{"location":"version-specific/supported-software/p/py-aiger/","title":"py-aiger","text":"A python library for manipulating sequential and combinatorial circuits. This module provides the py-aiger extensions: aiger_bv, aiger_cnf, aiger_ptltl, aiger_coins, aiger_gridworld, aiger_dfa
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homepage: https://pypi.org/project/python-Levenshtein/
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","boost":0.5},{"location":"version-specific/supported-software/p/python-blosc/","title":"python-blosc","text":"A Python wrapper for the extremely fast Blosc compression library.
homepage: https://github.com/Blosc/python-blosc/
version toolchain 1.11.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/python-casacore/","title":"python-casacore","text":"Python-casacore is a set of Python bindings for casacore, a c++ library used in radio astronomy. Python-casacore replaces the old pyrap.
homepage: https://casacore.github.io/python-casacore/#
version toolchain 3.5.2 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/python-docx/","title":"python-docx","text":"python-docx is a Python library for creating and updating Microsoft Word (.docx) files
homepage: https://python-docx.readthedocs.io/en/latest/
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","boost":0.5},{"location":"version-specific/supported-software/p/python-elf/","title":"python-elf","text":"Utils and convenience functions for large-scale bio-image analysis.
homepage: https://github.com/constantinpape/elf
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","boost":0.5},{"location":"version-specific/supported-software/p/python-hl7/","title":"python-hl7","text":"A simple library for parsing messages of Health Level 7 (HL7) version 2.x into Python objects.
homepage: https://github.com/johnpaulett/python-hl7
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","boost":0.5},{"location":"version-specific/supported-software/p/python-igraph/","title":"python-igraph","text":"Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis.
homepage: https://igraph.org/python
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","boost":0.5},{"location":"version-specific/supported-software/p/python-irodsclient/","title":"python-irodsclient","text":"A python API for iRODS
homepage: https://github.com/irods/python-irodsclient
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","boost":0.5},{"location":"version-specific/supported-software/p/python-isal/","title":"python-isal","text":"Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library.
homepage: https://github.com/pycompression/python-isal
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","boost":0.5},{"location":"version-specific/supported-software/p/python-libsbml/","title":"python-libsbml","text":"LibSBML Python API.
homepage: https://sbml.org/
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","boost":0.5},{"location":"version-specific/supported-software/p/python-louvain/","title":"python-louvain","text":"Louvain algorithm for community detection
homepage: https://pypi.org/project/python-louvain
version toolchain 0.15 foss/2021b 0.16 foss/2022a 0.16 foss/2022b 0.16 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/python-mujoco/","title":"python-mujoco","text":"This package is the canonical Python bindings for the MuJoCo physics engine. The mujoco package provides direct access to raw MuJoCo C API functions, structs, constants, and enumerations. Structs are provided as Python classes, with Pythonic initialization and deletion semantics.
homepage: https://www.mujoco.org
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","boost":0.5},{"location":"version-specific/supported-software/p/python-parasail/","title":"python-parasail","text":"This package contains Python bindings for parasail.
homepage: https://pypi.org/project/parasail/
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","boost":0.5},{"location":"version-specific/supported-software/p/python-telegram-bot/","title":"python-telegram-bot","text":"This library provides a pure Python, asynchronous interface for the Telegram Bot API. It's compatible with Python versions 3.7+.
homepage: https://python-telegram-bot.org/
version toolchain 20.0a0 GCCcore/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/p/python-weka-wrapper3/","title":"python-weka-wrapper3","text":"Python3 wrapper for the Weka Machine Learning Workbench
homepage: https://github.com/fracpete/python-weka-wrapper3
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","boost":0.5},{"location":"version-specific/supported-software/p/python-xxhash/","title":"python-xxhash","text":"Python bindings for xxHash. xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit.
homepage: https://github.com/ifduyue/python-xxhash
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","boost":0.5},{"location":"version-specific/supported-software/p/pythran/","title":"pythran","text":"Pythran is an ahead of time compiler for a subset of the Python language, with a focus on scientific computing. It takes a Python module annotated with a few interface description and turns it into a native Python module with the same interface, but (hopefully) faster.
homepage: https://pythran.readthedocs.io
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","boost":0.5},{"location":"version-specific/supported-software/p/pytorch-3dunet/","title":"pytorch-3dunet","text":"PyTorch implementation of 3D U-Net and its variants: - UNet3D: Standard 3D U-Net based on 3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation - ResidualUNet3D: Residual 3D U-Net based on Superhuman Accuracy on the SNEMI3D Connectomics Challenge - ResidualUNetSE3D: Similar to ResidualUNet3D with the addition of Squeeze and Excitation blocks based on Deep Learning Semantic Segmentation for High- Resolution Medical Volumes. Original squeeze and excite paper: Squeeze-and- Excitation Networks The code allows for training the U-Net for both: semantic segmentation (binary and multi-class) and regression problems (e.g. de-noising, learning deconvolutions).
homepage: https://github.com/wolny/pytorch-3dunet
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","boost":0.5},{"location":"version-specific/supported-software/p/pytorch-CycleGAN-pix2pix/","title":"pytorch-CycleGAN-pix2pix","text":"PyTorch implementations for both unpaired and paired image-to-image translation.
homepage: https://github.com/junyanz/pytorch-CycleGAN-and-pix2pix
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","boost":0.5},{"location":"version-specific/supported-software/q/","title":"List of supported software (q)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- q2-krona
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- qcint
- QCxMS
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- QGIS
- Qhull
- QIIME
- QIIME2
- Qiskit
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- Qt5
- Qt5Webkit
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(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/Q6/","title":"Q6","text":"EVB, FEP and LIE simulator.
homepage: https://github.com/qusers/Q6
version toolchain 20180205 gompi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/QCA/","title":"QCA","text":"Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.
homepage: https://github.com/KDE/qca
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","boost":0.5},{"location":"version-specific/supported-software/q/QCG-PilotJob/","title":"QCG-PilotJob","text":"A python service for easy execution of many tasks inside a single allocation.
homepage: https://qcg-pilotjob.readthedocs.org
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","boost":0.5},{"location":"version-specific/supported-software/q/QCxMS/","title":"QCxMS","text":"QCxMS is a quantum chemical based program to calculate electron ionization (EI) and collision induced dissociation (CID) mass spectra using Born-Oppenheimer Molecular Dynamics (BO-MD). It is the successor of the QCEIMS program, in which the EI part is exchanged to x to account for the greater general applicibility of the program.
homepage: https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms.html
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","boost":0.5},{"location":"version-specific/supported-software/q/QD/","title":"QD","text":"QD-Engineering Python Library for CAE
homepage: https://pypi.org/project/qd/
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","boost":0.5},{"location":"version-specific/supported-software/q/QDD/","title":"QDD","text":"A user-friendly program to select microsatellite markers and design primers from large sequencing projects.
homepage: http://net.imbe.fr/~emeglecz/qdd.html
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","boost":0.5},{"location":"version-specific/supported-software/q/QEMU/","title":"QEMU","text":"QEMU is a generic and open source machine emulator and virtualizer.
homepage: https://www.qemu.org/
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","boost":0.5},{"location":"version-specific/supported-software/q/QGIS/","title":"QGIS","text":"QGIS is a user friendly Open Source Geographic Information System (GIS)
homepage: http://www.qgis.org/
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","boost":0.5},{"location":"version-specific/supported-software/q/QIIME/","title":"QIIME","text":"QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
homepage: http://qiime.org/
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","boost":0.5},{"location":"version-specific/supported-software/q/QIIME2/","title":"QIIME2","text":"QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
homepage: http://qiime2.org/
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","boost":0.5},{"location":"version-specific/supported-software/q/QJson/","title":"QJson","text":"QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa.
homepage: http://qjson.sourceforge.net/
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","boost":0.5},{"location":"version-specific/supported-software/q/QML/","title":"QML","text":"QML is a Python2/3-compatible toolkit for representation learning of properties of molecules and solids.
homepage: https://www.qmlcode.org
version versionsuffix toolchain 0.2.10 -Python-2.7.13 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/QScintilla/","title":"QScintilla","text":"QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control
homepage: https://www.riverbankcomputing.com/software/qscintilla
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","boost":0.5},{"location":"version-specific/supported-software/q/QTLtools/","title":"QTLtools","text":"QTLtools is a tool set for molecular QTL discovery and analysis. It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps.
homepage: https://qtltools.github.io/qtltools/
version toolchain 1.1 intel/2016b 1.3.1 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/QUAST/","title":"QUAST","text":"QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison.
homepage: https://github.com/ablab/quast
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","boost":0.5},{"location":"version-specific/supported-software/q/Qhull/","title":"Qhull","text":"Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull.
homepage: http://www.qhull.org
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","boost":0.5},{"location":"version-specific/supported-software/q/Qiskit/","title":"Qiskit","text":"Qiskit is an open-source framework for working with noisy quantum computers at the level of pulses, circuits, and algorithms.
homepage: https://qiskit.org
version versionsuffix toolchain 0.11.1 -Python-3.7.2 foss/2019a 0.12.0 -Python-3.7.2 foss/2019a 0.31.0 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/Qt/","title":"Qt","text":"Qt is a comprehensive cross-platform C++ application framework.
homepage: http://qt.io/
version versionsuffix toolchain 3.3.8 intel/2016a 4.8.6 system 4.8.7 GCCcore/8.2.0 4.8.7 -GLib-2.48.0 foss/2016a 4.8.7 foss/2016a 4.8.7 foss/2016b 4.8.7 foss/2017a 4.8.7 foss/2017b 4.8.7 foss/2018a 4.8.7 foss/2018b 4.8.7 fosscuda/2018b 4.8.7 gimkl/2.11.5 4.8.7 -GLib-2.48.0 intel/2016a 4.8.7 intel/2016a 4.8.7 intel/2016b 4.8.7 intel/2017a 4.8.7 intel/2017b 4.8.7 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/Qt5/","title":"Qt5","text":"Qt is a comprehensive cross-platform C++ application framework.
homepage: https://qt.io/
version toolchain 5.10.1 foss/2018a 5.10.1 foss/2018b 5.10.1 fosscuda/2018b 5.10.1 intel/2018a 5.10.1 intel/2018b 5.11.2 foss/2018b 5.12.3 GCCcore/8.2.0 5.13.1 GCCcore/8.3.0 5.14.1 GCCcore/9.3.0 5.14.2 GCCcore/10.2.0 5.15.10 GCCcore/12.3.0 5.15.13 GCCcore/13.2.0 5.15.2 GCCcore/10.3.0 5.15.2 GCCcore/11.2.0 5.15.5 GCCcore/11.3.0 5.15.7 GCCcore/12.2.0 5.6.0 foss/2016a 5.6.0 intel/2016a 5.7.0 foss/2016a 5.7.0 foss/2016b 5.7.0 intel/2016a 5.7.0 intel/2016b 5.7.1 intel/2016b 5.8.0 foss/2017a 5.8.0 foss/2017b 5.8.0 intel/2016b 5.8.0 intel/2017a 5.8.0 intel/2017b 5.9.3 foss/2017b 5.9.8 fosscuda/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/Qt5Webkit/","title":"Qt5Webkit","text":"Qt Port of WebKit. WebKit is an open source web browser engine.
homepage: https://github.com/qt/qtwebkit
version toolchain 5.212.0-alpha3 GCCcore/8.2.0 5.212.0-alpha4 GCCcore/10.2.0 5.212.0-alpha4 GCCcore/11.2.0 5.212.0-alpha4 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/Qt6/","title":"Qt6","text":"Qt is a comprehensive cross-platform C++ application framework.
homepage: https://qt.io/
version toolchain 6.5.2 GCCcore/12.3.0 6.6.3 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/QtKeychain/","title":"QtKeychain","text":"Platform-independent Qt API for storing passwords securely.
homepage: https://github.com/frankosterfeld/qtkeychain
version toolchain 0.13.2 GCCcore/11.2.0 0.9.1 GCCcore/8.2.0 0.9.1 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/QtPy/","title":"QtPy","text":"QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide.
homepage: https://github.com/spyder-ide/qtpy
version versionsuffix toolchain 1.9.0 GCCcore/10.2.0 1.9.0 -Python-3.7.4 GCCcore/8.3.0 2.2.1 GCCcore/11.2.0 2.3.0 GCCcore/11.3.0 2.4.1 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/Qtconsole/","title":"Qtconsole","text":"A rich Qt-based console for working with Jupyter kernels, supporting rich media output, session export, and more. The Qtconsole is a very lightweight application that largely feels like a terminal, but provides a number of enhancements only possible in a GUI, such as inline figures, proper multiline editing with syntax highlighting, graphical calltips, and more.
homepage: https://jupyter.org/
version versionsuffix toolchain 4.7.7 -Python-3.7.4 foss/2019b 4.7.7 -Python-3.7.4 fosscuda/2019b 5.0.2 GCCcore/10.2.0 5.3.2 GCCcore/11.2.0 5.4.0 GCCcore/11.3.0 5.5.1 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/QuPath/","title":"QuPath","text":"QuPath is open source software for bioimage analysis. QuPath is often used for digital pathology applications because it offers a powerful set of tools for working with whole slide images - but it can be applied to lots of other kinds of image as well.
homepage: https://qupath.github.io
version versionsuffix toolchain 0.5.0 -Java-17 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/QuTiP/","title":"QuTiP","text":"QuTiP is open-source software for simulating the dynamics of open quantum systems.
homepage: http://qutip.org
version versionsuffix toolchain 4.1.0 -Python-2.7.12 intel/2016b 4.3.1 -Python-3.6.6 foss/2018b 4.3.1 -Python-3.6.6 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/QuaZIP/","title":"QuaZIP","text":"QuaZIP is the C++ wrapper for Gilles Vollant's ZIP/UNZIP package (AKA Minizip) using Trolltech's Qt library.
homepage: https://stachenov.github.io/quazip
version toolchain 0.8.1 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/Qualimap/","title":"Qualimap","text":"Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
homepage: http://qualimap.bioinfo.cipf.es/
version versionsuffix toolchain 2.2.1 -R-3.6.0 foss/2019a 2.2.1 -R-4.0.3 foss/2020b 2.2.1 -R-4.1.2 foss/2021b 2.3 -R-4.2.2 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/Quandl/","title":"Quandl","text":"A Python library for Quandl\u2019s RESTful API.
homepage: https://pypi.python.org/pypi/Quandl
version versionsuffix toolchain 3.4.2 -Python-3.6.4 intel/2018a 3.4.8 foss/2019a 3.6.1 foss/2020b 3.6.1 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/QuantumESPRESSO/","title":"QuantumESPRESSO","text":"Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).
homepage: https://www.quantum-espresso.org
version versionsuffix toolchain 5.3.0 intel/2016.02-GCC-4.9 5.4.0 -hybrid foss/2016b 5.4.0 intel/2016.02-GCC-4.9 6.0 intel/2016b 6.1 intel/2017a 6.2 intel/2017b 6.2.1 iomkl/2017b 6.3 foss/2018b 6.3 intel/2018b 6.4.1 intel/2019a 6.5 intel/2019a 6.5 intel/2019b 6.6 foss/2019b 6.6 foss/2020a 6.6 foss/2020b 6.6 intel/2019b 6.6 intel/2020a 6.7 foss/2019b 6.7 foss/2020b 6.7 foss/2021a 6.7 intel/2019b 6.7 intel/2021a 6.7 iomkl/2019b 6.8 foss/2021a 6.8 foss/2021b 6.8 intel/2021a 7.0 foss/2021b 7.0 intel/2021b 7.1 foss/2022a 7.1 intel/2022a 7.2 foss/2022b 7.2 foss/2023a 7.2 intel/2022b 7.3 foss/2023a 7.3 intel/2023a 7.3.1 foss/2023a 7.3.1 intel/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/QuickFF/","title":"QuickFF","text":"QuickFF is a Python package developed at the Center for Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio calculations.
homepage: http://molmod.github.io/QuickFF/
version versionsuffix toolchain 2.1.4 -Python-2.7.12 intel/2016b 2.2.0 -Python-2.7.14 intel/2017b 2.2.4 -Python-3.7.2 intel/2019a 2.2.4 -Python-3.8.2 intel/2020a 2.2.7 foss/2023a 2.2.7 -Python-3.8.2 intel/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/QuickPIC/","title":"QuickPIC","text":"QuickPIC is a 3D parallel (MPI & OpenMP Hybrid) Quasi-Static PIC code, which is developed based on the framework UPIC. QuickPIC can efficiently simulate plasma based accelerator problems. This is the UCLA Plasma Simulation Group's official open-source repository for QuickPIC.
homepage: https://github.com/UCLA-Plasma-Simulation-Group/QuickPIC-OpenSource
version toolchain 20210224 gompi/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/QuickTree/","title":"QuickTree","text":"QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe.
homepage: https://github.com/khowe/quicktree
version toolchain 2.5 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/Quip/","title":"Quip","text":"Quip compresses next-generation sequencing data with extreme prejudice. It supports input and output in the FASTQ and SAM/BAM formats, compressing large datasets to as little as 15% of their original size.
homepage: http://homes.cs.washington.edu/~dcjones/quip
version toolchain 1.1.8 GCC/4.8.2 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/Quorum/","title":"Quorum","text":"QuorUM is an error corrector for Illumina reads
homepage: http://www.genome.umd.edu/quorum.html
version toolchain 1.1.1 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/Qwt/","title":"Qwt","text":"The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background.
homepage: http://qwt.sourceforge.net/
version toolchain 6.1.2 intel/2016a 6.1.3 foss/2016b 6.1.3 intel/2016b 6.1.4 GCCcore/8.2.0 6.1.4 GCCcore/8.3.0 6.1.4 foss/2018b 6.1.5 GCCcore/10.2.0 6.1.5 GCCcore/9.3.0 6.2.0 GCCcore/10.3.0 6.2.0 GCCcore/11.2.0 6.2.0 GCCcore/12.2.0 6.3.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/QwtPolar/","title":"QwtPolar","text":"The QwtPolar library contains classes for displaying values on a polar coordinate system.
homepage: http://qwtpolar.sourceforge.net/
version toolchain 1.1.1 GCCcore/10.2.0 1.1.1 GCCcore/8.2.0 1.1.1 foss/2016b 1.1.1 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/q2-krona/","title":"q2-krona","text":"QIIME2 plugin for creating Krona plots
homepage: https://library.qiime2.org/plugins/q2-krona/39/
version toolchain 20220124 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/qcat/","title":"qcat","text":"qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files
homepage: https://github.com/nanoporetech/qcat/releases
version versionsuffix toolchain 1.1.0 -Python-3.7.4 foss/2019b 1.1.0 foss/2022b 1.1.0 foss/2023a 1.1.0 -Python-3.7.4 intel/2019b 1.1.0 -Python-3.8.2 intel/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/qcint/","title":"qcint","text":"libcint is an open source library for analytical Gaussian integrals. qcint is an optimized libcint branch for the x86-64 platform.
homepage: http://wiki.sunqm.net/libcint
version toolchain 3.0.18 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/qforce/","title":"qforce","text":"Quantum Mechanically augmented molecular force fields. Q-Force is a software package for deriving all-atom force fields from quantum mechanical calculations in an automated manner.
homepage: https://github.com/selimsami/qforce
version toolchain 0.6.11 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/qmflows/","title":"qmflows","text":"This library tackles the construction and efficient execution of computational chemistry workflows. This allows computational chemists to use the emerging massively parallel compute environments in an easy manner and focus on interpretation of scientific data rather than on tedious job submission procedures and manual data processing.
homepage: https://github.com/SCM-NV/qmflows
version toolchain 1.0.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/qnorm/","title":"qnorm","text":"Fast-ish (and correct!) quantile normalization in Python
homepage: https://github.com/Maarten-vd-Sande/qnorm
version toolchain 0.8.1 foss/2022a 0.8.1 foss/2022b 0.8.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/qpth/","title":"qpth","text":"A fast and differentiable QP solver for PyTorch.
homepage: https://locuslab.github.io/qpth/
version versionsuffix toolchain 0.0.13-20190626 -Python-3.7.2 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/qrupdate/","title":"qrupdate","text":"qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.
homepage: https://sourceforge.net/projects/qrupdate/
version toolchain 1.1.2 GCC/5.4.0-2.26 1.1.2 GCC/8.2.0-2.31.1 1.1.2 GCCcore/10.2.0 1.1.2 GCCcore/11.2.0 1.1.2 GCCcore/11.3.0 1.1.2 GCCcore/6.4.0 1.1.2 GCCcore/8.3.0 1.1.2 foss/2016a 1.1.2 foss/2018a 1.1.2 foss/2018b 1.1.2 intel/2016a 1.1.2 intel/2016b 1.1.2 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/q/qtop/","title":"qtop","text":"qtop is a nifty command-line tool for monitoring queueing systems, esp. PBS/torque. It tries to fit as much information as possible in your screen's real estate, by stitching together the output of commands like pbsnodes -a, qstat & qstat -q. It is possible to write wrappers for other platforms -people have done so for SGE, OAR etc- or, even examine traces offline and present the sampled information.
homepage: http://cern.ch/fotis/QTOP/
version versionsuffix toolchain 53 -1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/","title":"List of supported software (r)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- R
- R-bundle-Bioconductor
- R-bundle-CRAN
- R-INLA
- R-keras
- R-MXM
- R-opencv
- R-tesseract
- R-transport
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- Ragout
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- RAxML-NG
- Ray-assembler
- Ray-project
- Raysect
- RBFOpt
- RCall
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- Rcorrector
- RcppGSL
- rCUDA
- RDFlib
- RDKit
- RDP-Classifier
- RE2
- re2c
- Reads2snp
- Reapr
- ReaxFF
- RECON
- Red
- Redis
- redis-py
- Redland
- Redundans
- ReFrame
- Regenie
- regionmask
- RegTools
- Relate
- RELION
- remake
- ReMatCh
- REMORA
- renderproto
- RepastHPC
- RepeatMasker
- RepeatModeler
- RepeatScout
- request
- requests
- RERconverge
- ResistanceGA
- resolos
- Restrander
- rethinking
- retworkx
- RevBayes
- RFdiffusion
- rgdal
- rgeos
- Rgurobi
- rhdf5
- RHEIA
- RheoTool
- Rhodium
- rickflow
- RInChI
- rioxarray
- ripunzip
- rising
- Rivet
- rjags
- RLCard
- rmarkdown
- Rmath
- rMATS-long
- rMATS-turbo
- RMBlast
- RNA-Bloom
- RNA-SeQC
- RNAclust
- RNAcode
- RNAIndel
- RNAmmer
- rnamotif
- rnaQUAST
- RNAz
- RnBeads
- Roary
- ROCm
- rocm-cmake
- ROCm-CompilerSupport
- rocm-smi
- rocminfo
- ROCR-Runtime
- ROCT-Thunk-Interface
- ROI_PAC
- ROME
- ROOT
- root_numpy
- rootpy
- Rosetta
- rpmrebuild
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- rpy2
- RQGIS3
- RSEM
- RSeQC
- RStan
- rstanarm
- RStudio-Server
- RTG-Tools
- Rtree
- ruamel.yaml
- Ruby
- Ruby-Tk
- ruffus
- ruptures
- Rust
- rustworkx
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/R-INLA/","title":"R-INLA","text":"R-INLA is a package in R that do approximate Bayesian inference for Latent Gaussian Models.
homepage: https://www.r-inla.org
version versionsuffix toolchain 21.05.02 -R-4.0.4 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/R-MXM/","title":"R-MXM","text":"MXM: Feature Selection (Including Multiple Solutions) and Bayesian Networks
homepage: https://cran.r-project.org/package=MXM
version toolchain 1.5.5 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/R-bundle-Bioconductor/","title":"R-bundle-Bioconductor","text":"Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.
homepage: https://bioconductor.org
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","boost":0.5},{"location":"version-specific/supported-software/r/R-bundle-CRAN/","title":"R-bundle-CRAN","text":"Bundle of R packages from CRAN
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version toolchain 2023.12 foss/2023a 2024.06 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/R-keras/","title":"R-keras","text":"Interface to 'Keras' https://keras.io, a high-level neural networks 'API'.
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","boost":0.5},{"location":"version-specific/supported-software/r/R-opencv/","title":"R-opencv","text":"Experimenting with computer vision and machine learning in R. This package exposes some of the available OpenCV algorithms, such as edge, body or face detection. These can either be applied to analyze static images, or to filter live video footage from a camera device.
homepage: https://cran.r-project.org/web/packages/opencv/
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","boost":0.5},{"location":"version-specific/supported-software/r/R-tesseract/","title":"R-tesseract","text":"The R extension for using tesseract
homepage: https://cran.r-project.org/package=tesseract
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","boost":0.5},{"location":"version-specific/supported-software/r/R-transport/","title":"R-transport","text":"transport: Computation of Optimal Transport Plans and Wasserstein Distances
homepage: https://cran.r-project.org/package=transport
version toolchain 0.13-0 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/R/","title":"R","text":"R is a free software environment for statistical computing and graphics.
homepage: http://www.r-project.org/
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","boost":0.5},{"location":"version-specific/supported-software/r/R2jags/","title":"R2jags","text":"Providing wrapper functions to implement Bayesian analysis in JAGS.
homepage: https://cran.r-project.org/web/packages/R2jags
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","boost":0.5},{"location":"version-specific/supported-software/r/RAPSearch2/","title":"RAPSearch2","text":"RAPSearch stands for Reduced Alphabet based Protein similarity Search
homepage: https://omics.informatics.indiana.edu/mg/RAPSearch2
version toolchain 2.24 GCC/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/RASPA2/","title":"RASPA2","text":"A general purpose classical simulation package that can be used for the simulation of molecules in gases, fluids, zeolites, aluminosilicates, metal-organic frameworks, carbon nanotubes and external fields.
homepage: https://github.com/numat/RASPA2
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","boost":0.5},{"location":"version-specific/supported-software/r/RAxML-NG/","title":"RAxML-NG","text":"RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.
homepage: https://github.com/amkozlov/raxml-ng
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","boost":0.5},{"location":"version-specific/supported-software/r/RAxML/","title":"RAxML","text":"RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
homepage: https://github.com/stamatak/standard-RAxML
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","boost":0.5},{"location":"version-specific/supported-software/r/RBFOpt/","title":"RBFOpt","text":"RBFOpt is a Python library for black-box optimization (also known as derivative-free optimization).
homepage: https://github.com/coin-or/rbfopt
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","boost":0.5},{"location":"version-specific/supported-software/r/RCall/","title":"RCall","text":"This package facilitates communication between R and Julia and allows the user to call R packages from within Julia, providing the best of both worlds.
homepage: https://github.com/JuliaInterop/RCall.jl
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","boost":0.5},{"location":"version-specific/supported-software/r/RDFlib/","title":"RDFlib","text":"RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.
homepage: https://github.com/RDFLib/rdflib
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","boost":0.5},{"location":"version-specific/supported-software/r/RDKit/","title":"RDKit","text":"RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
homepage: https://www.rdkit.org
version versionsuffix toolchain 2018.09.3 -Python-3.6.6 intel/2018b 2019.09.3 -Python-3.7.4 foss/2019b 2020.03.3 -Python-3.8.2 foss/2020a 2020.03.3 -Python-3.8.2 intel/2020a 2020.09.3 -Python-3.7.4 foss/2019b 2021.03.4 foss/2021a 2022.03.5 foss/2021b 2022.09.4 foss/2022a 2023.03.3 foss/2021a 2024.03.3 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/RDP-Classifier/","title":"RDP-Classifier","text":"The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.
homepage: http://sourceforge.net/projects/rdp-classifier
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","boost":0.5},{"location":"version-specific/supported-software/r/RE2/","title":"RE2","text":"RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++ library.
homepage: https://github.com/google/re2
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","boost":0.5},{"location":"version-specific/supported-software/r/RECON/","title":"RECON","text":"Patched version of RECON to be used with RepeatModeler.
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","boost":0.5},{"location":"version-specific/supported-software/r/RELION/","title":"RELION","text":"RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).
homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
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","boost":0.5},{"location":"version-specific/supported-software/r/RFdiffusion/","title":"RFdiffusion","text":"RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges as we have outlined in the RFdiffusion paper.
homepage: https://github.com/RosettaCommons/RFdiffusion
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","boost":0.5},{"location":"version-specific/supported-software/r/RNA-SeQC/","title":"RNA-SeQC","text":"RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis.
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","boost":0.5},{"location":"version-specific/supported-software/r/RNAIndel/","title":"RNAIndel","text":"RNAIndel calls coding indels and classifies them into somatic, germline, and artifact from tumor RNA-Seq data.
homepage: https://github.com/stjude/RNAIndel
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","boost":0.5},{"location":"version-specific/supported-software/r/RNAclust/","title":"RNAclust","text":"RNAclust is a perl script summarizing all the single steps required for clustering of structured RNA motifs, i.e. identifying groups of RNA sequences sharing a secondary structure motif. It requires as input a multiple FASTA file.
homepage: http://www.bioinf.uni-leipzig.de/~kristin/Software/RNAclust/
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","boost":0.5},{"location":"version-specific/supported-software/r/RNAcode/","title":"RNAcode","text":"RNAcode - Analyze the protein coding potential in multiple sequence alignments
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","boost":0.5},{"location":"version-specific/supported-software/r/RNAmmer/","title":"RNAmmer","text":"This is an example description.
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","boost":0.5},{"location":"version-specific/supported-software/r/RNAz/","title":"RNAz","text":"RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.
homepage: http://www.tbi.univie.ac.at/~wash/RNAz/
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","boost":0.5},{"location":"version-specific/supported-software/r/ROCT-Thunk-Interface/","title":"ROCT-Thunk-Interface","text":"The user-mode API interfaces used to interact with the ROCk driver
homepage: https://github.com/RadeonOpenCompute/ROCT-Thunk-Interface
version toolchain 4.5.0 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/ROCm-CompilerSupport/","title":"ROCm-CompilerSupport","text":"The compiler support repository provides various Lightning Compiler related services
homepage: https://github.com/RadeonOpenCompute/ROCm-CompilerSupport
version toolchain 4.5.0 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/ROCm/","title":"ROCm","text":"AMD ROCm is the first open-source software development platform for HPC/Hyperscale-class GPU computing. AMD ROCm brings the UNIX philosophy of choice, minimalism and modular software development to GPU computing.
homepage: https://rocmdocs.amd.com/en/latest/
version toolchain 4.5.0 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/ROI_PAC/","title":"ROI_PAC","text":"Repeat Orbit Interferometry PACkage (ROI_PAC), software for processing synthetic aperture radar data to produce differential interferograms
homepage: http://roipac.org/
version versionsuffix toolchain 3.0.1 -Perl-5.24.1 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/ROME/","title":"ROME","text":"The ROME (Refinement and Optimization via Machine Learning for cryo-EM) Software package is one of the major research products at the Intel\u00ae PCCSB.
homepage: https://ipccsb.dfci.harvard.edu/rome
version toolchain 1.1.2 intel/2019.02 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/ROOT/","title":"ROOT","text":"The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way.
homepage: http://root.cern.ch/drupal/
version versionsuffix toolchain 6.10.02 -Python-2.7.12 foss/2016b 6.10.02 -Python-2.7.12 intel/2016b 6.10.04 -Python-2.7.13 intel/2017a 6.10.08 -Python-2.7.14 foss/2017b 6.10.08 -Python-2.7.14 intel/2017b 6.14.06 -Python-2.7.15 foss/2018b 6.14.06 -Python-3.6.6 foss/2018b 6.20.04 -Python-3.7.4 foss/2019b 6.22.08 foss/2020b 6.24.06 foss/2021b 6.26.06 foss/2022a 6.26.10 foss/2022b 6.30.06 foss/2023a v5.34.34 -Python-2.7.11 intel/2016a v5.34.36 -Python-2.7.11 intel/2016a v6.06.02 -Python-2.7.12 intel/2016b v6.08.02 -Python-2.7.11 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/RPostgreSQL/","title":"RPostgreSQL","text":"Database interface and 'PostgreSQL' driver for 'R'. This package provides a Database Interface 'DBI' compliant driver for 'R' to access 'PostgreSQL' database systems.
homepage: https://cran.r-project.org/package=tesseract
version toolchain 0.7-5 foss/2022a 0.7-6 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/RQGIS3/","title":"RQGIS3","text":"RQGIS3 establishes an interface between R and QGIS3, i.e., it allows the user to access QGIS3 functionalities from within R.
homepage: https://github.com/r-spatial/RQGIS3
version versionsuffix toolchain 20190903 -R-3.6.0 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/RSEM/","title":"RSEM","text":"RNA-Seq by Expectation-Maximization)
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version toolchain 1.2.26 GNU/4.9.3-2.25 1.2.30 foss/2016a 1.2.30 intel/2016b 1.3.0 foss/2016b 1.3.0 intel/2017a 1.3.1 foss/2017b 1.3.1 intel/2017b 1.3.1 intel/2018a 1.3.2 foss/2018b 1.3.3 foss/2019b 1.3.3 foss/2021b 1.3.3 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/RSeQC/","title":"RSeQC","text":"RSeQC provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.
homepage: http://rseqc.sourceforge.net/
version versionsuffix toolchain 2.6.4 -Python-2.7.12-R-3.3.1 foss/2016b 2.6.4 -Python-2.7.14 intel/2018a 3.0.0 -Python-3.6.6 foss/2018b 4.0.0 -Python-3.8.2 foss/2020a 4.0.0 foss/2021a 4.0.0 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/RStan/","title":"RStan","text":"RStan is the R interface to Stan. Stan is a state-of-the-art platform for statistical modeling and high-performance statistical computation.
homepage: https://github.com/stan-dev/rstan
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","boost":0.5},{"location":"version-specific/supported-software/r/RStudio-Server/","title":"RStudio-Server","text":"This is the RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R)
homepage: https://www.rstudio.com/
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","boost":0.5},{"location":"version-specific/supported-software/r/RTG-Tools/","title":"RTG-Tools","text":"RTG Tools contains utilities to easily manipulate and accurately compare multiple VCF files, as well as utilities for processing other common NGS data formats.
homepage: https://www.realtimegenomics.com/products/rtg-tools
version versionsuffix toolchain 3.12.1 -Java-11 system 3.9.1 -Java-1.8 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/RaGOO/","title":"RaGOO","text":"A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome
homepage: https://github.com/malonge/RaGOO
version versionsuffix toolchain 1.11 -Python-3.6.6 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Racon/","title":"Racon","text":"Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
homepage: https://github.com/isovic/racon
version toolchain 1.3.2 GCCcore/8.2.0 1.4.10 GCC/7.3.0-2.30 1.4.13 GCCcore/8.3.0 1.4.13 GCCcore/9.3.0 1.4.21 GCCcore/10.2.0 1.4.21 GCCcore/10.3.0 1.4.7 GCCcore/8.2.0 1.4.7 gcccuda/2019b 1.5.0 GCCcore/11.2.0 1.5.0 GCCcore/11.3.0 1.5.0 GCCcore/12.2.0 1.5.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/RagTag/","title":"RagTag","text":"RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: homology-based misassembly correction, homology-based assembly scaffolding and patching, and scaffold merging. RagTag also provides command line utilities for working with common genome assembly file formats.
homepage: https://github.com/malonge/RagTag
version toolchain 2.0.1 foss/2020b 2.1.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Ragout/","title":"Ragout","text":"Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome assembly using multiple references. Given a set of assembly fragments (contigs/scaffolds) and one or multiple related references (complete or draft), it produces a chromosome-scale assembly (as a set of scaffolds).
homepage: http://fenderglass.github.io/Ragout/
version versionsuffix toolchain 2.0 -Python-2.7.12 foss/2016b 2.3 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/RapidJSON/","title":"RapidJSON","text":"A fast JSON parser/generator for C++ with both SAX/DOM style API
homepage: https://rapidjson.org
version toolchain 1.1.0-20230928 GCCcore/12.3.0 1.1.0-20240409 GCCcore/13.2.0 1.1.0-20240815 GCCcore/13.3.0 1.1.0 GCCcore/10.2.0 1.1.0 GCCcore/10.3.0 1.1.0 GCCcore/11.2.0 1.1.0 GCCcore/11.3.0 1.1.0 GCCcore/12.2.0 1.1.0 GCCcore/12.3.0 1.1.0 GCCcore/8.2.0 1.1.0 GCCcore/8.3.0 1.1.0 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Raptor/","title":"Raptor","text":"Set of parsers and serializers that generate Resource Description Framework (RDF) triples by parsing syntaxes or serialize the triples into a syntax.
homepage: https://librdf.org/raptor/
version toolchain 2.0.16 GCCcore/10.3.0 2.0.16 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Rascaf/","title":"Rascaf","text":"Rascaf (RnA-seq SCAFfolder) uses continuity and order information from paired-end RNA-seq reads to improve a draft assembly, particularly in the gene regions.
homepage: https://github.com/mourisl/Rascaf
version toolchain 1.0.2 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Rasqal/","title":"Rasqal","text":"A library handling RDF query syntaxes, construction and execution
homepage: version toolchain 0.9.33 GCCcore/12.3.0
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Ratatosk/","title":"Ratatosk","text":"Phased hybrid error correction of long reads using colored de Bruijn graphs
homepage: https://github.com/DecodeGenetics/Ratatosk
version toolchain 0.4 GCC/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Raven/","title":"Raven","text":"Raven is a de novo genome assembler for long uncorrected reads.
homepage: https://github.com/lbcb-sci/raven
version toolchain 1.8.1 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Ray-assembler/","title":"Ray-assembler","text":"Parallel genome assemblies for parallel DNA sequencing
homepage: http://denovoassembler.sourceforge.net/
version toolchain 2.3.1 iimpi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Ray-project/","title":"Ray-project","text":"Ray is a fast and simple framework for building and running distributed applications.
homepage: https://docs.ray.io/en/latest/
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","boost":0.5},{"location":"version-specific/supported-software/r/Raysect/","title":"Raysect","text":"Raysect is an OOP ray-tracing framework for Python
homepage: https://raysect.org
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","boost":0.5},{"location":"version-specific/supported-software/r/Rcorrector/","title":"Rcorrector","text":"Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.
homepage: https://github.com/mourisl/Rcorrector
version toolchain 1.0.2 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/RcppGSL/","title":"RcppGSL","text":"The 'RcppGSL' package provides an easy-to-use interface between 'GSL' data structures and R using concepts from 'Rcpp' which is itself a package that eases the interfaces between R and C++.
homepage: https://cran.r-project.org/web/packages/RcppGSL
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","boost":0.5},{"location":"version-specific/supported-software/r/ReFrame/","title":"ReFrame","text":"ReFrame is a framework for writing regression tests for HPC systems.
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","boost":0.5},{"location":"version-specific/supported-software/r/ReMatCh/","title":"ReMatCh","text":"Reads mapping against target sequences, checking mapping and consensus sequences production
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","boost":0.5},{"location":"version-specific/supported-software/r/Reads2snp/","title":"Reads2snp","text":"reads2snp is a SNP and genotype caller: it predicts the genotype of distinct individuals at distinct positions of a set of sequences based on read mapping / read counts. Its typical input is a bam file. Its typical output is a vcf file. It is written in C++, based on the bio++ libraries, multi-threaded with openMP, available under Linux and MacOS
homepage: http://kimura.univ-montp2.fr/PopPhyl/index.php?section=tools
version toolchain 2.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Reapr/","title":"Reapr","text":"A tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison.
homepage: https://www.sanger.ac.uk/science/tools/reapr
version toolchain 1.0.18 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/ReaxFF/","title":"ReaxFF","text":"parameter generation code for the REAXFF Reactive force field program
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","boost":0.5},{"location":"version-specific/supported-software/r/Red/","title":"Red","text":"Red (REpeat Detector)
homepage: http://toolsmith.ens.utulsa.edu/
version toolchain 2015-05-22 iccifort/2019.1.144-GCC-8.2.0-2.31.1 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Redis/","title":"Redis","text":"Redis is an open source (BSD licensed), in-memory data structure store, used as a database, cache, and message broker. Redis provides data structures such as strings, hashes, lists, sets, sorted sets with range queries, bitmaps, hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, Lua scripting, LRU eviction, transactions, and different levels of on-disk persistence, and provides high availability via Redis Sentinel and automatic partitioning with Redis Cluster.
homepage: https://redis.io
version toolchain 6.2.6 GCC/10.3.0 6.2.6 GCC/11.2.0 7.0.8 GCC/11.3.0 7.2.3 GCCcore/12.3.0 7.2.4 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Redland/","title":"Redland","text":"Redland is a set of free software C libraries that provide support for the Resource Description Framework (RDF).
homepage: https://librdf.org/raptor
version toolchain 1.0.17 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Redundans/","title":"Redundans","text":"Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
homepage: https://github.com/lpryszcz/redundans
version toolchain 0.13c intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/RegTools/","title":"RegTools","text":"RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
homepage: https://regtools.readthedocs.org
version toolchain 0.4.2 foss/2020b 0.5.2 foss/2020b 0.5.2 foss/2021b 1.0.0 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Regenie/","title":"Regenie","text":"Regenie is a C++ program for whole genome regression modelling of large genome-wide association studies. It is developed and supported by a team of scientists at the Regeneron Genetics Center.
homepage: https://rgcgithub.github.io/regenie
version toolchain 3.1.2 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/Relate/","title":"Relate","text":"Software for estimating genome-wide genealogies for thousands of samples
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version versionsuffix toolchain 20211123 -R-4.0.3 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/RepastHPC/","title":"RepastHPC","text":"The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers.
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version toolchain 2.2.0 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/RepeatMasker/","title":"RepeatMasker","text":"RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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","boost":0.5},{"location":"version-specific/supported-software/r/RepeatModeler/","title":"RepeatModeler","text":"RepeatModeler is a de novo transposable element (TE) family identification and modeling package.
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homepage: https://github.com/mritchielab/restrander
version toolchain 20230713 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 1.1.1 GCC/10.2.0 1.1.1 GCC/11.2.0 1.2.1 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://github.com/fppimenta/rheoTool
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homepage: https://github.com/Project-Platypus/Rhodium
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homepage: https://gitlab.com/hepcedar/rivet
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homepage: https://rnbeads.org
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homepage: https://www.rosettacommons.org
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homepage: https://toblerity.org/rtree/
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homepage: https://github.com/randy3k/radian
version toolchain 0.6.9 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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","boost":0.5},{"location":"version-specific/supported-software/r/randfold/","title":"randfold","text":"Minimum free energy of folding randomization test software
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homepage: https://rapidtide.readthedocs.io
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homepage: https://github.com/perrygeo/python-rasterstats
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homepage: https://gitlab.unige.ch/resolos/resolos
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","boost":0.5},{"location":"version-specific/supported-software/r/rethinking/","title":"rethinking","text":"R package that contains tools for conducting both quick quadratic approximation of the posterior distribution as well as Hamiltonian Monte Carlo.
homepage: https://github.com/rmcelreath/rethinking
version versionsuffix toolchain 2.40-20230914 -R-4.3.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/retworkx/","title":"retworkx","text":"retworkx is a general purpose graph library for python3 written in Rust to take advantage of the performance and safety that Rust provides. It was built as a replacement for qiskit's previous (and current) networkx usage (hence the name) but is designed to provide a high performance general purpose graph library for any python application. The project was originally started to build a faster directed graph to use as the underlying data structure for the DAG at the center of qiskit-terra's transpiler, but it has since grown to cover all the graph usage in Qiskit and other applications.
homepage: https://github.com/Qiskit/retworkx
version toolchain 0.9.0 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rgdal/","title":"rgdal","text":"Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the 'PROJ.4' library.
homepage: http://rgdal.r-forge.r-project.org/
version versionsuffix toolchain 1.4-4 -R-3.6.0 foss/2019a 1.4-8 -R-3.6.2 foss/2019b 1.4-8 -R-4.0.0 foss/2020a 1.5-16 -R-4.0.0 foss/2020a 1.5-23 -R-4.0.4 foss/2020b 1.5-23 -R-4.1.0 foss/2021a 1.6-6 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rgeos/","title":"rgeos","text":"R interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries
homepage: https://cran.r-project.org/web/packages/rgeos/
version versionsuffix toolchain 0.3-17 -R-3.2.3 intel/2016a 0.5-1 -R-3.6.0 foss/2019a 0.5-2 -R-3.6.2 foss/2019b 0.5-5 -R-4.0.0 foss/2020a 0.5-5 -R-4.1.0 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rhdf5/","title":"rhdf5","text":"This R/Bioconductor package provides an interface between HDF5 and R.
homepage: https://bioconductor.org/packages/release/bioc/html/rhdf5.html
version versionsuffix toolchain 2.16.0 -R-3.2.3 intel/2016a 2.18.0 -R-3.3.1 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rickflow/","title":"rickflow","text":"Running and Analyzing OpenMM Jobs
homepage: https://gitlab.com/Olllom/rickflow
version versionsuffix toolchain 0.7.0-20200529 -Python-3.7.4 intel/2019b 0.7.0 -Python-3.7.4 intel/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rioxarray/","title":"rioxarray","text":"geospatial xarray extension powered by rasterio
homepage: https://github.com/corteva/rioxarray
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","boost":0.5},{"location":"version-specific/supported-software/r/ripunzip/","title":"ripunzip","text":"A tool to unzip files in parallel.
homepage: https://github.com/google/ripunzip
version toolchain 0.4.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rising/","title":"rising","text":"Provides everything needed for high performance data loading and augmentation in PyTorch.
homepage: https://rising.rtfd.io/
version versionsuffix toolchain 0.2.2 -CUDA-11.3.1 foss/2021a 0.2.2 foss/2021a 0.2.2 -CUDA-11.7.0 foss/2022a 0.2.2 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rjags/","title":"rjags","text":"The rjags package is an interface to the JAGS library.
homepage: https://cran.r-project.org/web/packages/rjags
version versionsuffix toolchain 4-10 foss/2019b 4-10 -R-4.0.0 foss/2020a 4-10 -R-4.0.3 foss/2020b 4-10 -R-4.0.4 foss/2020b 4-10 -R-4.0.5 foss/2020b 4-10 -R-4.1.0 foss/2021a 4-10 -R-4.0.3 fosscuda/2020b 4-10 -R-4.0.4 fosscuda/2020b 4-10 -R-4.0.5 fosscuda/2020b 4-12 -R-4.1.2 foss/2021b 4-13 -R-4.2.1 foss/2022a 4-13 -R-4.2.2 foss/2022b 4-15 -R-4.3.2 foss/2023a 4-6 -R-3.4.0 intel/2017a 4-6 -R-3.4.3 intel/2017b 4-8 -R-3.5.1 foss/2018b 4-9 -R-3.6.0 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rmarkdown/","title":"rmarkdown","text":"Convert R Markdown documents into a variety of formats.
homepage: https://cran.r-project.org/web/packages/rmarkdown
version versionsuffix toolchain 2.20 -R-4.1.0 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rnaQUAST/","title":"rnaQUAST","text":"rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.
homepage: https://cab.spbu.ru/software/rnaquast/
version versionsuffix toolchain 1.5.2 -Python-2.7.15 foss/2018b 2.2.0 -Python-3.8.2 foss/2020a 2.2.2 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rnamotif/","title":"rnamotif","text":"The rnamotif program searchs input sequences for portions that match a given descriptor or \"motif\". Matching sequences can also be ranked by various scoring functions.
homepage: https://github.com/dacase/rnamotif
version toolchain 20240904 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rocm-cmake/","title":"rocm-cmake","text":"ROCM cmake modules provides cmake modules for common build tasks needed for the ROCM software stack
homepage: https://github.com/RadeonOpenCompute/rocm-cmake
version toolchain 4.5.0 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rocm-smi/","title":"rocm-smi","text":"The ROCm System Management Interface Library, or ROCm SMI library, is part of the Radeon Open Compute ROCm software stack. It is a C library for Linux that provides a user space interface for applications to monitor and control GPU applications.
homepage: https://github.com/RadeonOpenCompute/rocm_smi_lib
version toolchain 4.5.0 GCCcore/11.2.0 5.4.4 GCCcore/11.3.0 5.6.0 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rocminfo/","title":"rocminfo","text":"ROCm Application for Reporting System Info
homepage: https://github.com/RadeonOpenCompute/rocminfo
version toolchain 4.5.0 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/root_numpy/","title":"root_numpy","text":"root_numpy is a Python extension module that provides an efficient interface between ROOT and NumPy. root_numpy\u2019s internals are compiled C++ and can therefore handle large amounts of data much faster than equivalent pure Python implementations.
homepage: https://scikit-hep.org/root_numpy/
version versionsuffix toolchain 4.8.0 -Python-3.6.6 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rootpy/","title":"rootpy","text":"The rootpy project is a community-driven initiative aiming to provide a more pythonic interface with ROOT on top of the existing PyROOT bindings. Given Python\u2019s reflective and dynamic nature, rootpy also aims to improve ROOT design flaws and supplement existing ROOT functionality. The scientific Python community also offers a multitude of powerful packages such as SciPy, NumPy, matplotlib, scikit-learn, and PyTables, but a suitable interface between them and ROOT has been lacking. rootpy provides the interfaces and conversion mechanisms required to liberate your data and to take advantage of these alternatives if needed.
homepage: http://www.rootpy.org/
version versionsuffix toolchain 0.8.0 -Python-2.7.11 foss/2016a 1.0.1 -Python-3.6.6 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rpmrebuild/","title":"rpmrebuild","text":"rpmrebuild is a tool to build an RPM file from a package that has already been installed in a basic use
homepage: http://rpmrebuild.sourceforge.net/
version toolchain 2.11 system 2.18 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rpy2/","title":"rpy2","text":"rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions.
homepage: http://rpy.sourceforge.net/
version versionsuffix toolchain 2.7.9 -Python-2.7.12 foss/2016b 2.8.2 -Python-2.7.13 intel/2017a 3.2.6 -Python-3.7.4 foss/2019b 3.4.5 foss/2021a 3.4.5 foss/2021b 3.5.15 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rstanarm/","title":"rstanarm","text":"Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation.
homepage: https://r-forge.r-project.org/projects/rstanarm
version versionsuffix toolchain 2.19.3 -R-3.6.2 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/ruamel.yaml/","title":"ruamel.yaml","text":"ruamel.yaml is a YAML 1.2 loader/dumper package for Python.
homepage: https://sourceforge.net/projects/ruamel-yaml
version toolchain 0.17.21 GCCcore/10.3.0 0.17.21 GCCcore/11.2.0 0.17.21 GCCcore/11.3.0 0.17.21 GCCcore/12.2.0 0.17.32 GCCcore/12.3.0 0.18.6 GCCcore/13.2.0 0.18.6 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/ruffus/","title":"ruffus","text":"Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly, and widely used in science and bioinformatics.
homepage: http://www.ruffus.org.uk/
version toolchain 2.8.4 GCCcore/11.3.0 2.8.4 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/ruptures/","title":"ruptures","text":"ruptures is a Python library for off-line change point detection. This package provides methods for the analysis and segmentation of non-stationary signals. Implemented algorithms include exact and approximate detection for various parametric and non-parametric models. ruptures focuses on ease of use by providing a well-documented and consistent interface. In addition, thanks to its modular structure, different algorithms and models can be connected and extended within this package.
homepage: https://github.com/deepcharles/ruptures/
version toolchain 1.1.8 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/r/rustworkx/","title":"rustworkx","text":"rustworkx (previously retworkx) is a general purpose graph library for Python written in Rust to take advantage of the performance and safety that Rust provides. It is designed to provide a high performance general purpose graph library for any Python application.
homepage: https://github.com/Qiskit/rustworkx
version toolchain 0.12.1 foss/2022a 0.12.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/","title":"List of supported software (s)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- S-Lang
- s3fs
- S4
- Sabre
- safestringlib
- Safetensors
- SAGE
- Sagemath
- Sailfish
- SALib
- Salmon
- SALMON-TDDFT
- Sambamba
- samblaster
- Samcef
- samclip
- samplot
- SAMtools
- sansa
- SAP
- SAS
- Satsuma2
- savvy
- Saxon-HE
- SBCL
- sbt
- ScaFaCoS
- ScaLAPACK
- Scalasca
- SCALCE
- Scalene
- scanpy
- scArches
- scCODA
- scCustomize
- sceasy
- SCENIC
- SCENICplus
- scFEA
- scGeneFit
- SCGid
- scGSVA
- scHiCExplorer
- Schrodinger
- scib
- scib-metrics
- sciClone
- ScientificPython
- scikit-allel
- scikit-bio
- scikit-build
- scikit-build-core
- scikit-cuda
- scikit-extremes
- scikit-image
- scikit-learn
- scikit-lego
- scikit-misc
- scikit-multilearn
- scikit-optimize
- scikit-plot
- scikit-uplift
- SCIP
- SCIPhI
- scipy
- SciPy-bundle
- SciTools-Iris
- SCnorm
- Scoary
- SCons
- SCOOP
- SCopeLoomR
- Score-P
- SCOTCH
- scp
- scPred
- Scrappie
- SCReadCounts
- scrublet
- scVelo
- scvi-tools
- Scythe
- SDCC
- SDL
- SDL2
- SDL2_gfx
- SDL2_image
- SDL2_mixer
- SDL2_ttf
- SDL_image
- SDSL
- sdsl-lite
- Seaborn
- SEACells
- SearchGUI
- SeaView
- SECAPR
- Seeder
- segemehl
- segment-anything
- segmentation-models
- segmentation-models-pytorch
- SeisSol
- SelEstim
- SELFIES
- SemiBin
- semla
- Sentence-Transformers
- SentencePiece
- sentinelsat
- sep
- SEPP
- Seq-Gen
- seq2HLA
- SeqAn
- SeqAn3
- SeqKit
- SeqLib
- Seqmagick
- SeqPrep
- seqtk
- Serf
- setuptools
- setuptools-rust
- Seurat
- SeuratData
- SeuratDisk
- SeuratWrappers
- sf
- sfftk
- Shannon
- SHAP
- shapAAR
- SHAPEIT
- SHAPEIT4
- Shapely
- SharedMeatAxe
- sharutils
- Shasta
- ShengBTE
- shift
- SHORE
- Short-Pair
- shovill
- shrinkwrap
- SHTns
- Sibelia
- SICER2
- sickle
- Siesta
- SignalP
- silhouetteRank
- silx
- simanneal
- simint
- SimNIBS
- SimPEG
- SIMPLE
- Simple-DFTD3
- SimpleElastix
- SimpleITK
- simpy
- Simstrat
- SimVascular
- Single-cell-python-bundle
- SingleM
- Singular
- sinto
- SiNVICT
- SIONlib
- SIP
- SIRIUS
- sirocco
- siscone
- SISSO
- SISSO++
- SKA2
- SKESA
- sketchmap
- skewer
- sklearn-pandas
- sklearn-som
- skorch
- sktime
- SlamDunk
- SLATEC
- SLEPc
- slepc4py
- sleuth
- slidingwindow
- SLiM
- slow5tools
- slurm-drmaa
- smafa
- smallgenomeutilities
- SMAP
- SMARTdenovo
- SMC++
- smfishHmrf
- smithwaterman
- Smoldyn
- smooth-topk
- SMRT-Link
- SMV
- snakemake
- SNAP
- SNAP-ESA
- SNAP-ESA-python
- SNAP-HMM
- SNAPE-pooled
- snaphu
- snappy
- Sniffles
- snippy
- snp-sites
- snpEff
- SNPhylo
- SNPomatic
- SOAPaligner
- SOAPdenovo-Trans
- SOAPdenovo2
- SOAPfuse
- socat
- SOCI
- SolexaQA++
- solo
- sonic
- SoPlex
- SoQt
- SortMeRNA
- SoupX
- SoX
- SoXt
- SpaceRanger
- Spack
- spaCy
- SPAdes
- spaln
- Spark
- sparse-neighbors-search
- sparsehash
- SpatialDE
- spatialreg
- spdlog
- SpectrA
- spectral.methods
- speech_tools
- SPEI
- spektral
- SpFFT
- spglib
- spglib-python
- Sphinx
- Sphinx-RTD-Theme
- SpiceyPy
- SpiecEasi
- spla
- SplAdder
- SPLASH
- SpliceMap
- split-seq
- splitRef
- SPM
- spoa
- SPOOLES
- SPOTPY
- SPRNG
- Spyder
- SQLAlchemy
- SQLite
- SqueezeMeta
- Squidpy
- SRA-Toolkit
- sradownloader
- SRPRISM
- SRST2
- SSAHA2
- SSN
- SSPACE_Basic
- SSW
- Stable-Baselines3
- STACEY
- Stack
- Stacks
- STAMP
- StaMPS
- Stampy
- STAR
- STAR-CCM+
- STAR-Fusion
- stardist
- starparser
- stars
- Stata
- Statistics-R
- statsmodels
- STEAK
- STIR
- stpipeline
- strace
- Strainberry
- STREAM
- strelka
- StringTie
- stripy
- STRique
- Structure
- Structure_threader
- STRUMPACK
- suave
- SuAVE-biomat
- submitit
- Subread
- subset-bam
- subunit
- Subversion
- suds
- SuiteSparse
- SUMACLUST
- SUMATRA
- SUMO
- SUNDIALS
- SunPy
- SuperLU
- SuperLU_DIST
- supermagic
- supernova
- SUPPA
- SURVIVOR
- SVclone
- SVDetect
- SVDquest
- SVDSS2
- SVG
- SVIM
- svist4get
- swarm
- SWASH
- SWAT+
- swifter
- SWIG
- SWIPE
- swissknife
- SymEngine
- SymEngine-python
- SYMMETRICA
- SYMPHONY
- sympy
- synapseclient
- synthcity
- SyRI
- sysbench
- Szip
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/S-Lang/","title":"S-Lang","text":"S-Lang is a multi-platform programmer's library designed to allow a developer to create robust multi-platform software. It provides facilities required by interactive applications such as display/screen management, keyboard input, keymaps, and so on.
homepage: http://www.jedsoft.org/slang/
version toolchain 2.3.0 GCC/4.9.2 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/S4/","title":"S4","text":"S4 stands for Stanford Stratified Structure Solver, a frequency domain code to solve the linear Maxwell\u2019s equations in layered periodic structures. Internally, it uses Rigorous Coupled Wave Analysis (RCWA, also called the Fourier Modal Method (FMM)) and the S-matrix algorithm.
homepage: https://web.stanford.edu/group/fan/S4
version toolchain 1.1.1-20180610 foss/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SAGE/","title":"SAGE","text":"S.A.G.E. (Statistical Analysis for Genetic Epidemiology) is free software package containing programs for use in the genetic analysis of family, pedigree and individual data.
homepage: http://darwin.cwru.edu/sage/
version toolchain 6.3 system 6.4 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SALMON-TDDFT/","title":"SALMON-TDDFT","text":"SALMON is an open-source computer program for ab-initio quantum-mechanical calculations of electron dynamics at the nanoscale that takes place in various situations of light-matter interactions. It is based on time-dependent density functional theory, solving time-dependent Kohn-Sham equation in real time and real space with norm-conserving pseudopotentials.
homepage: https://salmon-tddft.jp
version toolchain 1.2.1 foss/2018b 1.2.1 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SALib/","title":"SALib","text":"Sensitivity Analysis Library in Python (Numpy). Contains Sobol, Morris, Fractional Factorial and FAST methods.
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","boost":0.5},{"location":"version-specific/supported-software/s/SAMtools/","title":"SAMtools","text":"SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
homepage: http://www.htslib.org/
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version toolchain 1.1.3 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SAS/","title":"SAS","text":"SAS is a software suite for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.
homepage: https://www.sas.com
version toolchain 9.4 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 2.0.9 GCCcore/9.3.0 2.2.1 GCCcore/10.3.0 2.3.11 GCCcore/11.3.0 2.4.1 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 2.7 GCC/4.8.2 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://scenic.aertslab.org
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","boost":0.5},{"location":"version-specific/supported-software/s/SCENICplus/","title":"SCENICplus","text":"SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
homepage: https://github.com/aertslab/scenicplus
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version toolchain 0.9b0 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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version toolchain 3.2.1 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://github.com/cbg-ethz/SCIPhI
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homepage: http://pyscoop.org
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homepage: https://horvathlab.github.io/NGS/SCReadCounts/
version toolchain 1.4.0 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://bioconductor.org/packages/SCnorm
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homepage: https://github.com/aertslab/SCopeLoomR
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homepage: https://github.com/libsdl-org/SDL_mixer
version toolchain 2.6.3 GCCcore/11.3.0 2.8.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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","boost":0.5},{"location":"version-specific/supported-software/s/SDL_image/","title":"SDL_image","text":"SDL_image is an image file loading library.
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version toolchain 1.2.12 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://github.com/simongog/sdsl-lite
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version toolchain 20230731 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://bitbucket.org/nschaeff/shtns
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","boost":0.5},{"location":"version-specific/supported-software/s/SICER2/","title":"SICER2","text":"Redesigned and improved ChIP-seq broad peak calling tool SICER
homepage: https://zanglab.github.io/SICER2/
version versionsuffix toolchain 1.0.3 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SIMPLE/","title":"SIMPLE","text":"Single-particle IMage Processing Linux Engine is a program package for cryo-EM image processing, focusing on ab initio 3D reconstruction of low-symmetry single-particles.
homepage: http://simplecryoem.com/
version toolchain 2.5 foss/2018a 3.0.0 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SIONlib/","title":"SIONlib","text":"SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version.
homepage: http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html
version versionsuffix toolchain 1.6.1 -tools foss/2016a 1.6.1 foss/2016a 1.7.1 -tools foss/2017a 1.7.1 foss/2017a 1.7.4 -tools GCCcore/8.2.0 1.7.6 -tools GCCcore/10.2.0 1.7.6 -tools GCCcore/10.3.0 1.7.6 -tools GCCcore/8.3.0 1.7.6 -tools GCCcore/9.3.0 1.7.7 -tools GCCcore/11.2.0 1.7.7 -tools GCCcore/11.3.0 1.7.7 -tools GCCcore/12.2.0 1.7.7 -tools GCCcore/12.3.0 1.7.7 -tools GCCcore/13.2.0 1.7.7 -tools GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SIP/","title":"SIP","text":"SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.
homepage: http://www.riverbankcomputing.com/software/sip/
version versionsuffix toolchain 4.18 -Python-2.7.11 foss/2016a 4.18 -Python-2.7.11 intel/2016a 4.18.1 -Python-2.7.11 foss/2016a 4.18.1 -Python-2.7.12 intel/2016b 4.19 -Python-2.7.12 foss/2016b 4.19 -Python-2.7.12 intel/2016b 4.19.13 -Python-2.7.15 fosscuda/2018b 4.19.2 -Python-2.7.13 intel/2017a 4.19.8 -Python-2.7.14 foss/2017b 4.19.8 -Python-2.7.14 foss/2018a 4.19.8 -Python-3.6.4 foss/2018a 4.19.8 -Python-2.7.14 intel/2017b 4.19.8 -Python-2.7.14 intel/2018a 4.19.8 -Python-3.6.4 intel/2018a 6.8.1 GCCcore/12.3.0 6.8.3 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SIRIUS/","title":"SIRIUS","text":"SIRIUS is a domain specific library for electronic structure calculations. It implements pseudopotential plane wave (PP-PW) and full potential linearized augmented plane wave (FP-LAPW) methods.
homepage: https://github.com/electronic-structure/SIRIUS
version toolchain 7.5.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SISSO%2B%2B/","title":"SISSO++","text":"C++ implementation of SISSO with built in Python bindings for an efficient python interface
homepage: https://gitlab.com/sissopp_developers/sissopp
version toolchain 1.1 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SISSO/","title":"SISSO","text":"A data-driven method combining symbolic regression and compressed sensing toward accurate & interpretable models.
homepage: https://github.com/rouyang2017/SISSO
version toolchain 3.0.2 iimpi/2021b 3.1-20220324 iimpi/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SKA2/","title":"SKA2","text":"Split k-mer analysis (version 2) uses exact matching of split k-mer sequences to align closely related sequences, typically small haploid genomes such as bacteria and viruses.
homepage: https://docs.rs/ska/latest/ska/
version toolchain 0.3.7 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SKESA/","title":"SKESA","text":"SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs.
homepage: https://github.com/ncbi/SKESA
version versionsuffix toolchain 2.2 foss/2018a 2.3.0 foss/2018b 2.4.0 _saute.1.3.0_1 gompi/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SLATEC/","title":"SLATEC","text":"SLATEC Common Mathematical Library, a comprehensive software library containing over 1400 general purpose mathematical and statistical routines written in Fortran 77.
homepage: https://www.netlib.org/slatec/
version toolchain 4.1 GCC/6.4.0-2.28 4.1 GCC/8.3.0 4.1 iccifort/2018.1.163-GCC-6.4.0-2.28 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SLEPc/","title":"SLEPc","text":"SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.
homepage: https://slepc.upv.es/
version versionsuffix toolchain 3.11.0 foss/2018b 3.12.2 -Python-3.7.4 foss/2019b 3.12.2 -Python-3.8.2 foss/2020a 3.12.2 -Python-2.7.16 intel/2019b 3.12.2 -Python-3.7.4 intel/2019b 3.12.2 -Python-3.8.2 intel/2020a 3.14.2 foss/2020b 3.15.1 foss/2021a 3.17.2 foss/2022a 3.18.2 intel/2021b 3.20.1 foss/2023a 3.8.3 foss/2017b 3.9.2 foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SLiM/","title":"SLiM","text":"SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.
homepage: https://messerlab.org/slim
version toolchain 3.4 GCC/9.3.0 4.0 GCC/11.2.0 4.0.1 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SMAP/","title":"SMAP","text":"SMAP is an analysis tool for stack-based NGS read mapping
homepage: https://ngs-smap.readthedocs.io
version toolchain 4.6.5 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SMARTdenovo/","title":"SMARTdenovo","text":"SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from all-vs-all raw read alignments without an error correction stage. It also provides tools to generate accurate consensus sequences, though a platform dependent consensus polish tools (e.g. Quiver for PacBio or Nanopolish for ONT) are still required for higher accuracy.
homepage: https://github.com/ruanjue/smartdenovo
version toolchain 20180219 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SMC%2B%2B/","title":"SMC++","text":"SMC++ is a program for estimating the size history of populations from whole genome sequence data.
homepage: https://github.com/popgenmethods/smcpp
version toolchain 1.15.4 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SMRT-Link/","title":"SMRT-Link","text":"PacBio's open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided
homepage: https://www.pacb.com/support/software-downloads/
version versionsuffix toolchain 12.0.0.177059 -cli-tools-only system 5.1.0.26412 -cli-tools-only system 6.0.0.47841 -cli-tools-only system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SMV/","title":"SMV","text":"Smokeview is a visualization program that displays output of FDS and CFAST simulations.
homepage: https://github.com/firemodels/smv
version toolchain 6.7.17 iccifort/2020.4.304 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SNAP-ESA-python/","title":"SNAP-ESA-python","text":"Python interface to the Sentinel Application Platform (SNAP) API
homepage: https://step.esa.int/main/toolboxes/snap/
version versionsuffix toolchain 8.0 -Java-1.8-Python-2.7.18 GCCcore/10.2.0 9.0.0 -Java-11-Python-2.7.18 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SNAP-ESA/","title":"SNAP-ESA","text":"The Sentinel Application Platform (SNAP) is a common architecture for all Sentinel Toolboxes being jointly developed by Brockmann Consult, SkyWatch and C-S. The SNAP architecture is ideal for Earth Observation processing and analysis due to the following technological innovations: Extensibility, Portability, Modular Rich Client Platform, Generic EO Data Abstraction, Tiled Memory Management, and a Graph Processing Framework.
homepage: https://step.esa.int/main/toolboxes/snap/
version versionsuffix toolchain 10.0.0 -Java-11 system 8.0 -Java-1.8 system 9.0.0 -Java-11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SNAP-HMM/","title":"SNAP-HMM","text":"SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.
homepage: http://korflab.ucdavis.edu/software.html
version toolchain 2013-11-29 GCC/6.4.0-2.28 2013-11-29 GCC/8.3.0 2013-11-29 iccifort/2017.4.196-GCC-6.4.0-2.28 20190603 GCC/10.2.0 20221022 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SNAP/","title":"SNAP","text":"Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
homepage: http://snap.cs.berkeley.edu/
version toolchain 1.0beta.23 intel/2017b 2.0.1 GCC/11.2.0 2.0.1 GCC/11.3.0 2.0.1 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SNAPE-pooled/","title":"SNAPE-pooled","text":"\" SNAPE-pooled computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.
homepage: https://github.com/EmanueleRaineri/snape-pooled
version toolchain 20150707 GCC/11.3.0 r32 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SNPhylo/","title":"SNPhylo","text":"SNPhylo: a pipeline to generate a phylogenetic tree from huge SNP data
homepage: http://chibba.pgml.uga.edu/snphylo/
version versionsuffix toolchain 20140701 foss/2016a 20140701 intel/2016a 20160204 -Python-2.7.14-R-3.4.3 foss/2017b 20160204 -Python-2.7.14-R-3.4.3 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SNPomatic/","title":"SNPomatic","text":"High throughput sequencing technologies generate large amounts of short reads. Mapping these to a reference sequence consumes large amounts of processing time and memory, and read mapping errors can lead to noisy or incorrect alignments. SNP-o-matic is a fast, memory-efficient, and stringent read mapping tool offering a variety of analytical output functions, with an emphasis on genotyping.
homepage: https://github.com/magnusmanske/snpomatic
version toolchain 1.0 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SOAPaligner/","title":"SOAPaligner","text":"SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment.
homepage: http://soap.genomics.org.cn/soapaligner.html
version versionsuffix toolchain 2.21 _Linux-x86_64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SOAPdenovo-Trans/","title":"SOAPdenovo-Trans","text":"SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.
homepage: http://soap.genomics.org.cn/SOAPdenovo-Trans.html
version toolchain 1.0.4 intel/2017a 1.0.5 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SOAPdenovo2/","title":"SOAPdenovo2","text":"SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo.
homepage: http://soap.genomics.org.cn/index.html
version toolchain r240 GCC/5.4.0-2.26 r241 GCC/6.4.0-2.28 r241 foss/2018a r241 iccifort/2017.4.196-GCC-6.4.0-2.28 r241 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SOAPfuse/","title":"SOAPfuse","text":"SOAPfuse is an open source tool developed for genome-wide detection of fusion transcripts from paired-end RNA-Seq data.
homepage: https://sourceforge.net/p/soapfuse/wiki/Home/
version versionsuffix toolchain 1.27 -Perl-5.24.0 foss/2016b 1.27 -Perl-5.28.0 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SOCI/","title":"SOCI","text":"SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++.
homepage: http://soci.sourceforge.net/
version toolchain 4.0.1 GCC/10.2.0 4.0.1 GCCcore/9.3.0 4.0.2 GCC/10.3.0 4.0.3 GCC/11.2.0 4.0.3 GCC/11.3.0 4.0.3 GCC/12.2.0 4.0.3 GCC/12.3.0 4.0.3 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SPAdes/","title":"SPAdes","text":"Genome assembler for single-cell and isolates data sets
homepage: http://cab.spbu.ru/software/spades/
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","boost":0.5},{"location":"version-specific/supported-software/s/SPEI/","title":"SPEI","text":"A simple Python package to calculate drought indices for time series such as the SPI, SPEI and SGI.
homepage: https://github.com/martinvonk/spei
version toolchain 0.3.5 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SPLASH/","title":"SPLASH","text":"SPLASH is a free and open source visualisation tool for Smoothed Particle Hydrodynamics (SPH) simulations.
homepage: http://users.monash.edu.au/~dprice/splash/index.html
version toolchain 2.8.0 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SPM/","title":"SPM","text":"SPM (Statistical Parametric Mapping) refers to the construction and assessment of spatially extended statistical processes used to test hypo- theses about functional imaging data. These ideas have been instantiated in software that is called SPM. The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG.
homepage: https://www.fil.ion.ucl.ac.uk/spm
version versionsuffix toolchain 12.5_r7771 -MATLAB-2021a system 12.5_r7771 -MATLAB-2021b system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SPOOLES/","title":"SPOOLES","text":"SPOOLES is a library for solving sparse real and complex linear systems of equations, written in the C language using object oriented design.
homepage: https://netlib.org/linalg/spooles/spooles.2.2.html
version toolchain 2.2 gompi/2021a 2.2 gompi/2022b 2.2 gompi/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SPOTPY/","title":"SPOTPY","text":"SPOTPY is a Python framework that enables the use of Computational optimization techniques for calibration, uncertainty and sensitivity analysis techniques of almost every (environmental-) model.
homepage: https://spotpy.readthedocs.io
version toolchain 1.5.14 intel/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SPRNG/","title":"SPRNG","text":"Scalable Parallel Pseudo Random Number Generators Library
homepage: http://www.sprng.org/
version toolchain 2.0b foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SQLAlchemy/","title":"SQLAlchemy","text":"SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives application developers the full power and flexibility of SQL. SQLAlchemy provides a full suite of well known enterprise-level persistence patterns, designed for efficient and high-performing database access, adapted into a simple and Pythonic domain language.
homepage: https://www.sqlalchemy.org/
version toolchain 2.0.25 GCCcore/12.3.0 2.0.29 GCCcore/12.2.0 2.0.29 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SQLite/","title":"SQLite","text":"SQLite: SQL Database Engine in a C Library
homepage: http://www.sqlite.org/
version toolchain 3.13.0 GCC/4.9.3-2.25 3.13.0 GCC/5.4.0-2.26 3.13.0 GCCcore/6.3.0 3.13.0 foss/2016.04 3.13.0 foss/2016a 3.13.0 foss/2016b 3.13.0 iccifort/2016.3.210-GCC-5.4.0-2.26 3.13.0 intel/2016b 3.14.1 GCCcore/4.9.3 3.17.0 GCCcore/6.3.0 3.20.1 GCCcore/6.4.0 3.21.0 GCCcore/6.4.0 3.23.0 GCCcore/6.4.0 3.24.0 GCCcore/7.2.0 3.24.0 GCCcore/7.3.0 3.26.0 GCCcore/8.2.0 3.27.2 GCCcore/8.2.0 3.29.0 GCCcore/8.3.0 3.31.1 GCCcore/9.3.0 3.33.0 GCCcore/10.2.0 3.35.4 GCCcore/10.3.0 3.36 GCCcore/11.2.0 3.38.3 GCCcore/11.3.0 3.39.4 GCCcore/12.2.0 3.41.2 GCCcore/13.1.0 3.42.0 GCCcore/12.3.0 3.43.1 GCCcore/13.2.0 3.45.3 GCCcore/13.3.0 3.8.10.2 GCC/4.9.3-2.25 3.8.10.2 GNU/4.9.3-2.25 3.8.10.2 gimkl/2.11.5 3.8.8.1 GCC/4.8.4 3.8.8.1 GCC/4.9.2 3.9.2 GCC/4.9.3-2.25 3.9.2 foss/2016a 3.9.2 gimkl/2.11.5 3.9.2 intel/2016.02-GCC-4.9 3.9.2 intel/2016a 3.9.2 iomkl/2016.07 3.9.2 iomkl/2016.09-GCC-4.9.3-2.25 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SRA-Toolkit/","title":"SRA-Toolkit","text":"The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format
homepage: https://github.com/ncbi/sra-tools
version versionsuffix toolchain 2.10.4 gompi/2019b 2.10.5 -centos_linux64 system 2.10.8 gompi/2020a 2.10.9 gompi/2020b 2.3.5 -centos_linux64 system 2.5.4-1 -centos_linux64 system 2.5.7 -centos_linux64 system 2.8.2-1 -centos_linux64 system 2.9.0 -centos_linux64 system 2.9.2 -ubuntu64 system 2.9.4 -centos_linux64 system 2.9.6-1 -centos_linux64 system 3.0.0 -centos_linux64 system 3.0.0 gompi/2021b 3.0.10 gompi/2023a 3.0.3 gompi/2022a 3.0.5 gompi/2021a 3.0.5 gompi/2022b 3.1.1 gompi/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SRPRISM/","title":"SRPRISM","text":"Single Read Paired Read Indel Substitution Minimizer
homepage: https://github.com/ncbi/SRPRISM
version versionsuffix toolchain 3.0.0 foss/2018b 3.1.1 -Java-11 GCCcore/8.2.0 3.1.2 GCCcore/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SRST2/","title":"SRST2","text":"Short Read Sequence Typing for Bacterial Pathogens
homepage: https://katholt.github.io/srst2
version versionsuffix toolchain 0.2.0-20210620 -Python-2.7.18 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SSAHA2/","title":"SSAHA2","text":"SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences. SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package.
homepage: http://www.sanger.ac.uk/resources/software/ssaha2/
version versionsuffix toolchain 2.5.5 -i686 system 2.5.5 -x86_64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SSN/","title":"SSN","text":"Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included.
homepage: https://cran.r-project.org/web/packages/SSN
version versionsuffix toolchain 1.1.14 -R-3.6.0 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SSPACE_Basic/","title":"SSPACE_Basic","text":"SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension
homepage: https://github.com/nsoranzo/sspace_basic
version versionsuffix toolchain 2.1.1 -Python-2.7.18 GCC/10.2.0 2.1.1 -Perl-5.24.1 intel/2017a 2.1.1 -Perl-5.26.0 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SSW/","title":"SSW","text":"SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically.
homepage: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
version toolchain 1.1 GCCcore/10.2.0 1.1 GCCcore/10.3.0 1.1 GCCcore/11.2.0 1.1 GCCcore/12.3.0 1.1 GCCcore/9.3.0 1.2.4 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/STACEY/","title":"STACEY","text":"The BEAST2 package STACEY can be used for species delimitation and species tree estimation, based on the multispecies coalescent model.
homepage: http://www.indriid.com/software.html
version toolchain 1.2.5 GCC/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/STAMP/","title":"STAMP","text":"STAMP is a tool for characterizing similarities between transcription factor binding motifs
homepage: http://www.benoslab.pitt.edu/stamp/
version toolchain 1.2 intel/2016a 1.3 intel/2016a 1.3 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/STAR-CCM%2B/","title":"STAR-CCM+","text":"STAR-CCM+ is a complete multidisciplinary platform for the simulation of products and designs operating under real-world conditions.
homepage: https://mdx.plm.automation.siemens.com/star-ccm-plus
version versionsuffix toolchain 13.04.011 system 17.02.008 -r8 system 17.02.008 system 17.04.008 -r8 system 17.04.008 system 17.06.007 -r8 system 17.06.007 system 18.02.008 -r8 system 18.02.008 system 18.06.006 -r8 system 18.06.006 system 2302 -r8 system 2302 system 2310 -r8 system 2310 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/STAR-Fusion/","title":"STAR-Fusion","text":"STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.
homepage: https://github.com/STAR-Fusion/STAR-Fusion
version versionsuffix toolchain 1.5.0 -Perl-5.28.0 foss/2018b 1.6.0 -Perl-5.28.1-Python-3.7.2 GCC/8.2.0-2.31.1 1.8.1 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/STAR/","title":"STAR","text":"STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
homepage: https://github.com/alexdobin/STAR
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","boost":0.5},{"location":"version-specific/supported-software/s/STEAK/","title":"STEAK","text":"Detects integrations of any sort in high-throughput sequencing (HTS) data. STEAK was built for validating and discovering transposable element (TE) and retroviral integrations in a variety of HTS data. The software performs on both single-end (SE) and paired-end ( PE) libraries and on a variety of HTS sequencing strategies. It can be applied to a broad range of research interests and clinical uses such as population genetic studies and detecting polymorphic integrations.
homepage: https://omictools.com/steak-tool
version versionsuffix toolchain 2019.09.12 -Python-2.7.16 foss/2019b 2019.09.12 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/STIR/","title":"STIR","text":"Software for Tomographic Image Reconstruction
homepage: http://stir.sourceforge.net/
version toolchain 3.0 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/STREAM/","title":"STREAM","text":"The STREAM benchmark is a simple synthetic benchmark program that measures sustainable memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.
homepage: https://www.cs.virginia.edu/stream/
version toolchain 5.10 GCC/11.3.0 5.10 GCC/7.3.0-2.30 5.10 GCC/8.2.0-2.31.1 5.10 GCC/9.3.0 5.10 iccifort/2020.1.217 5.10 intel/2016b 5.10 intel/2018b 5.10 intel-compilers/2022.2.1 5.10 intel-compilers/2024.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/STRUMPACK/","title":"STRUMPACK","text":"STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner for both dense and sparse systems using low-rank structured factorization with randomized sampling.
homepage: https://fastmath-scidac.llnl.gov/software/strumpack.html
version toolchain 6.1.0 foss/2020b 6.1.0 intel/2020b 7.1.0 foss/2023b 7.1.0 intel/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/STRique/","title":"STRique","text":"STRique is a python package to analyze repeat expansion and methylation states of short tandem repeats (STR) in Oxford Nanopore Technology (ONT) long read sequencing data.
homepage: https://github.com/giesselmann/STRique
version toolchain 0.4.2 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SUMACLUST/","title":"SUMACLUST","text":"SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences.
homepage: http://metabarcoding.org/sumatra
version toolchain 1.0.20 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SUMATRA/","title":"SUMATRA","text":"SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences.
homepage: http://metabarcoding.org/sumatra
version toolchain 1.0.20 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SUMO/","title":"SUMO","text":"Simulation of Urban MObility\" (SUMO) is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large networks. It allows for intermodal simulation including pedestrians and comes with a large set of tools for scenario creation.
homepage: https://www.eclipse.org/sumo/
version versionsuffix toolchain 1.12.0 foss/2021b 1.14.1 foss/2021b 1.3.1 -Python-3.7.4 GCCcore/8.3.0 1.7.0 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SUNDIALS/","title":"SUNDIALS","text":"SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
homepage: http://computation.llnl.gov/projects/sundials
version versionsuffix toolchain 2.6.2 intel/2016b 2.6.2 intel/2018b 2.7.0 foss/2016b 2.7.0 foss/2017b 2.7.0 foss/2018a 2.7.0 foss/2018b 2.7.0 intel/2016b 2.7.0 intel/2017a 2.7.0 intel/2017b 2.7.0 intel/2018a 5.1.0 foss/2019b 5.1.0 intel/2019b 5.7.0 foss/2020b 5.7.0 fosscuda/2020b 5.7.0 intel/2020b 6.2.0 foss/2020b 6.2.0 intel/2020b 6.3.0 foss/2021b 6.3.0 foss/2022a 6.5.1 foss/2022a 6.6.0 foss/2022b 6.6.0 -CUDA-12.1.1 foss/2023a 6.6.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SUPPA/","title":"SUPPA","text":"Fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions.
homepage: https://github.com/comprna/SUPPA
version toolchain 2.3-20231005 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SURVIVOR/","title":"SURVIVOR","text":"Toolset for SV simulation, comparison and filtering
homepage: https://github.com/fritzsedlazeck/SURVIVOR
version toolchain 1.0.7-19-ged1ca51 GCC/11.2.0 1.0.7-19-ged1ca51 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SVDSS2/","title":"SVDSS2","text":"Improved structural variant discovery in accurate long reads using sample-specific strings (SFS).
homepage: https://github.com/Parsoa/SVDSS
version toolchain 2.0.0-alpha.3 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SVDetect/","title":"SVDetect","text":"SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identifying structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale.
homepage: http://svdetect.sourceforge.net/Site/Home.html
version versionsuffix toolchain 0.8b -Perl-5.26.0 GCC/6.4.0-2.28 0.8b -Perl-5.26.0 iccifort/2017.4.196-GCC-6.4.0-2.28 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SVDquest/","title":"SVDquest","text":"SVDquartets-based species trees
homepage: https://github.com/pranjalv123/SVDquest
version toolchain 20190627 gompi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SVG/","title":"SVG","text":"Perl binding for SVG
homepage: https://metacpan.org/pod/SVG
version versionsuffix toolchain 2.84 -Perl-5.30.0 foss/2019b 2.87 GCC/11.2.0 2.87 GCC/11.3.0 2.87 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SVIM/","title":"SVIM","text":"SVIM (pronounced swim) is a structural variant caller for third-generation sequencing reads. It is able to detect and classify the following six classes of structural variation: deletions, insertions, inversions, tandem duplications, interspersed duplications and translocations.
homepage: https://github.com/eldariont/svim
version toolchain 2.0.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SVclone/","title":"SVclone","text":"Cluster structural variants of similar cancer cell fraction (CCF).
homepage: https://github.com/mcmero/SVclone
version toolchain 1.1.2 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SWASH/","title":"SWASH","text":"SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces.
homepage: http://swash.sourceforge.net/
version versionsuffix toolchain 3.14 -mpi intel/2016b 3.14 -mpi intel/2017a 4.01 -mpi intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SWAT%2B/","title":"SWAT+","text":"The Soil & Water Assessment Tool (SWAT) is a small watershed to river basin-scale model used to simulate the quality and quantity of surface and ground water and predict the environmental impact of land use, land management practices, and climate change. In order to face present and future challenges in water resources modeling SWAT code has undergone major modifications over the past few years, resulting in SWAT+, a completely revised version of the model. SWAT+ provides a more flexible spatial representation of interactions and processes within a watershed.
homepage: https://swatplus.gitbook.io
version toolchain 60.4.1 GCC/9.3.0 60.5.1 iccifort/2020.4.304 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SWIG/","title":"SWIG","text":"SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
homepage: http://www.swig.org/
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","boost":0.5},{"location":"version-specific/supported-software/s/SWIPE/","title":"SWIPE","text":"Smith-Waterman database searches with inter-sequence SIMD parallelisation
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version toolchain 2.1.1 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SYMMETRICA/","title":"SYMMETRICA","text":"Symmetrica is a Collection of C routines for representation theory.
homepage: https://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA
version toolchain 2.0 GCCcore/11.3.0 2.0 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SYMPHONY/","title":"SYMPHONY","text":"SYMPHONY is an open-source solver for mixed-integer linear programs (MILPs) written in C.
homepage: https://projects.coin-or.org/SYMPHONY
version toolchain 5.6.16 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/Sabre/","title":"Sabre","text":"Sabre is a tool that will demultiplex barcoded reads into separate files. It will work on both single-end and paired-end data in fastq format. It simply compares the provided barcodes with each read and separates the read into its appropriate barcode file, after stripping the barcode from the read (and also stripping the quality values of the barcode bases).
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version toolchain 2013-09-28 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/Safetensors/","title":"Safetensors","text":"Safetensors is a new simple format for storing tensors safely (as opposed to pickle) and that is still fast (zero-copy). Safetensors is really fast.
homepage: https://huggingface.co/docs/safetensors
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","boost":0.5},{"location":"version-specific/supported-software/s/Sagemath/","title":"Sagemath","text":"Sage is open source mathematical software released under the GNU General Public Licence GPLv2+, and includes packages that have compatible software licenses. People all around the globe have contributed to the development of Sage. Full documentation is available online.
homepage: https://doc.sagemath.org/html/en/index.html
version toolchain 10.4 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/Sailfish/","title":"Sailfish","text":"Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of isoform abundances directly from a set of reference sequences and RNA-seq reads.
homepage: http://www.cs.cmu.edu/~ckingsf/software/sailfish/
version versionsuffix toolchain 0.10.1 -Python-2.7.12 foss/2016b 0.10.1 gompi/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/Salmon/","title":"Salmon","text":"Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
homepage: https://github.com/COMBINE-lab/salmon
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","boost":0.5},{"location":"version-specific/supported-software/s/Samcef/","title":"Samcef","text":"FEM solver solution suite for basic linear structures to advanced, flexible nonlinear mechanisms and thermal applications.
homepage: http://www.plm.automation.siemens.com/en_us/products/lms/samtech/samcef-solver-suite/
version toolchain 17.0-03 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/Satsuma2/","title":"Satsuma2","text":"Satsuma2 is an optimised version of Satsuma, a tool to reliably align large and complex DNA sequences providing maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accommodate the billions of base pairs in vertebrate genomes).
homepage: https://github.com/bioinfologics/satsuma2
version toolchain 20220304 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/Saxon-HE/","title":"Saxon-HE","text":"Open Source SAXON XSLT processor developed by Saxonica Limited.
homepage: http://saxon.sourceforge.net
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","boost":0.5},{"location":"version-specific/supported-software/s/ScaFaCoS/","title":"ScaFaCoS","text":"ScaFaCoS is a library of scalable fast coulomb solvers.
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version toolchain 1.0.1 foss/2020a 1.0.1 foss/2020b 1.0.1 foss/2021a 1.0.1 foss/2021b 1.0.1 intel/2020a 1.0.4 foss/2022a 1.0.4 foss/2022b 1.0.4 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/ScaLAPACK/","title":"ScaLAPACK","text":"The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
homepage: http://www.netlib.org/scalapack/
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","boost":0.5},{"location":"version-specific/supported-software/s/Scalasca/","title":"Scalasca","text":"Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks -- in particular those concerning communication and synchronization -- and offers guidance in exploring their causes.
homepage: http://www.scalasca.org/
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","boost":0.5},{"location":"version-specific/supported-software/s/Scalene/","title":"Scalene","text":"Scalene is a high-performance CPU, GPU and memory profiler for Python that does a number of things that other Python profilers do not and cannot do. It runs orders of magnitude faster than other profilers while delivering far more detailed information.
homepage: https://github.com/plasma-umass/scalene
version toolchain 1.5.13 GCCcore/11.2.0 1.5.20 GCCcore/11.3.0 1.5.26 GCCcore/12.2.0 1.5.26 GCCcore/12.3.0 1.5.35 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/Schrodinger/","title":"Schrodinger","text":"Schrodinger aims to provide integrated software solutions and services that truly meet its customers needs. We want to empower researchers around the world to achieve their goals of improving human health and quality of life through advanced computational techniques that transform the way chemists design compounds and materials.
homepage: https://www.schrodinger.com/
version toolchain 2020-4 system 2021-4 system 2022-1 system 2022-2 system 2022-3 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SciPy-bundle/","title":"SciPy-bundle","text":"Bundle of Python packages for scientific software
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","boost":0.5},{"location":"version-specific/supported-software/s/SciTools-Iris/","title":"SciTools-Iris","text":"A powerful, format-agnostic, community-driven Python package for analysing and visualising Earth science data.
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version toolchain 3.2.1 foss/2022a 3.9.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/ScientificPython/","title":"ScientificPython","text":"ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization.
homepage: http://dirac.cnrs-orleans.fr/ScientificPython
version versionsuffix toolchain 2.9.4 -Python-2.7.11 foss/2016a 2.9.4 -Python-2.7.11 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/Scoary/","title":"Scoary","text":"Microbial pan-GWAS using the output from Roary
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","boost":0.5},{"location":"version-specific/supported-software/s/Score-P/","title":"Score-P","text":"The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications.
homepage: http://www.score-p.org
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","boost":0.5},{"location":"version-specific/supported-software/s/Scrappie/","title":"Scrappie","text":"Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group.
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","boost":0.5},{"location":"version-specific/supported-software/s/Scythe/","title":"Scythe","text":"Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases.
homepage: https://github.com/ucdavis-bioinformatics/scythe
version toolchain 0.994 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SeaView/","title":"SeaView","text":"SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.
homepage: https://doua.prabi.fr/software/seaview
version toolchain 5.0.5 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/Seaborn/","title":"Seaborn","text":"Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics.
homepage: https://seaborn.pydata.org/
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","boost":0.5},{"location":"version-specific/supported-software/s/SearchGUI/","title":"SearchGUI","text":"SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines and de novo sequencing algorithms, currently supporting X! Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda, OMSSA, Novor and DirecTag.
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homepage: https://github.com/fritzsedlazeck/Sniffles
version toolchain 2.0.7 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SoPlex/","title":"SoPlex","text":"SoPlex is an optimization package for solving linear programming problems (LPs) based on an advanced implementation of the primal and dual revised simplex algorithm. It provides special support for the exact solution of LPs with rational input data. It can be used as a standalone solver reading MPS or LP format files via a command line interface as well as embedded into other programs via a C++ class library.
homepage: https://soplex.zib.de/
version toolchain 2.2.1 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SoQt/","title":"SoQt","text":"SoQt is a Qt GUI component toolkit library for Coin. It is also compatible with SGI and TGS Open Inventor, and the API is based on the API of the InventorXt GUI component toolkit.
homepage: https://coin3d.github.io/SoQt/html
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","boost":0.5},{"location":"version-specific/supported-software/s/SoX/","title":"SoX","text":"SoX is the Swiss Army Knife of sound processing utilities. It can convert audio files to other popular audio file types and also apply sound effects and filters during the conversion.
homepage: https://sourceforge.net/projects/sox
version toolchain 14.4.2 GCC/8.3.0 14.4.2 GCCcore/11.3.0 14.4.2 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SoXt/","title":"SoXt","text":"SoXt is an Xt/Motif glue library for Coin. It can also be used on top of the SGI or TGS implementation of Open Inventor, and is designed to be source code compatible with SGI's InventorXt library.
homepage: https://coin3d.github.io/SoXt/html/
version toolchain 1.4.0 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SolexaQA%2B%2B/","title":"SolexaQA++","text":"SolexaQA calculates sequence quality statistics and creates visual representations of data quality for second-generation sequencing data. Originally developed for the Illumina system (historically known as \u201cSolexa\u201d), SolexaQA now also supports Ion Torrent and 454 data.
homepage: http://solexaqa.sourceforge.net
version toolchain 3.1.5 foss/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SortMeRNA/","title":"SortMeRNA","text":"SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads.
homepage: https://bioinfo.lifl.fr/RNA/sortmerna/
version toolchain 2.1 GCC/9.3.0 2.1 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SoupX/","title":"SoupX","text":"\" Quantify, profile and remove ambient mRNA contamination (the \"soup\") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018) .
homepage: https://github.com/constantAmateur/SoupX
version versionsuffix toolchain 1.6.2 -R-4.2.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SpFFT/","title":"SpFFT","text":"Sparse 3D FFT library with MPI, OpenMP, CUDA and ROCm support.
homepage: https://github.com/eth-cscs/SpFFT/
version toolchain 1.1.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/SpaceRanger/","title":"SpaceRanger","text":"Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image.
homepage: https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger
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","boost":0.5},{"location":"version-specific/supported-software/s/Spack/","title":"Spack","text":"Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.
homepage: https://spack.io/
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","boost":0.5},{"location":"version-specific/supported-software/s/SpatialDE/","title":"SpatialDE","text":"SpatialDE is a method to identify genes which significantly depend on spatial coordinates in non-linear and non-parametric ways. The intended applications are spatially resolved RNA-sequencing from e.g. Spatial Transcriptomics, or in situ gene expression measurements from e.g. SeqFISH or MERFISH.
homepage: https://pypi.org/project/SpatialDE
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","boost":0.5},{"location":"version-specific/supported-software/s/SpectrA/","title":"SpectrA","text":"Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library.
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","boost":0.5},{"location":"version-specific/supported-software/s/Sphinx-RTD-Theme/","title":"Sphinx-RTD-Theme","text":"Sphinx theme designed to provide a great reader experience for documentation users on both desktop and mobile devices.
homepage: https://sphinx-rtd-theme.readthedocs.io
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","boost":0.5},{"location":"version-specific/supported-software/s/Sphinx/","title":"Sphinx","text":"Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. It was originally created for the new Python documentation, and it has excellent facilities for the documentation of Python projects, but C/C++ is already supported as well, and it is planned to add special support for other languages as well.
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","boost":0.5},{"location":"version-specific/supported-software/s/SpiceyPy/","title":"SpiceyPy","text":"SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (N65)
homepage: https://github.com/AndrewAnnex/SpiceyPy
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","boost":0.5},{"location":"version-specific/supported-software/s/SpiecEasi/","title":"SpiecEasi","text":"Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
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","boost":0.5},{"location":"version-specific/supported-software/s/SplAdder/","title":"SplAdder","text":"Splicing Adder is a toolbox for alternative splicing analysis based on RNA-Seq alignment data. Briefly, the software takes a given annotation and RNA-Seq read alignments in standardized formats, transforms the annotation into a splicing graph representation, augments the splicing graph with additional information extracted from the read data, extracts alternative splicing events from the graph and quantifies the events based on the alignment data.
homepage: https://github.com/ratschlab/spladder
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","boost":0.5},{"location":"version-specific/supported-software/s/SpliceMap/","title":"SpliceMap","text":"SpliceMap is a de novo splice junction discovery and alignment tool. It offers high sensitivity and support for arbitrary RNA-seq read lengths.
homepage: https://web.stanford.edu/group/wonglab/SpliceMap/
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","boost":0.5},{"location":"version-specific/supported-software/s/Spyder/","title":"Spyder","text":"Spyder is an interactive Python development environment providing MATLAB-like features in a simple and light-weighted software.
homepage: https://github.com/spyder-ide/spyder
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","boost":0.5},{"location":"version-specific/supported-software/s/SqueezeMeta/","title":"SqueezeMeta","text":"SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis.
homepage: https://github.com/jtamames/SqueezeMeta
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","boost":0.5},{"location":"version-specific/supported-software/s/Squidpy/","title":"Squidpy","text":"Squidpy is a tool for the analysis and visualization of spatial molecular data.
homepage: https://squidpy.readthedocs.io
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","boost":0.5},{"location":"version-specific/supported-software/s/StaMPS/","title":"StaMPS","text":"A software package to extract ground displacements from time series of synthetic aperture radar (SAR) acquisitions.
homepage: http://homepages.see.leeds.ac.uk/~earahoo/stamps/
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","boost":0.5},{"location":"version-specific/supported-software/s/Stable-Baselines3/","title":"Stable-Baselines3","text":"Stable Baselines3 (SB3) is a set of reliable implementations of reinforcement learning algorithms in PyTorch.
homepage: https://github.com/DLR-RM/stable-baselines3
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","boost":0.5},{"location":"version-specific/supported-software/s/Stack/","title":"Stack","text":"Stack is a cross-platform program for developing Haskell projects. It is intended for Haskellers both new and experienced.
homepage: https://docs.haskellstack.org
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","boost":0.5},{"location":"version-specific/supported-software/s/Stacks/","title":"Stacks","text":"Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
homepage: http://creskolab.uoregon.edu/stacks/
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","boost":0.5},{"location":"version-specific/supported-software/s/Stampy/","title":"Stampy","text":"Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome.
homepage: http://www.well.ox.ac.uk/stampy
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","boost":0.5},{"location":"version-specific/supported-software/s/Stata/","title":"Stata","text":"Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics.
homepage: https://www.stata.com/
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","boost":0.5},{"location":"version-specific/supported-software/s/Statistics-R/","title":"Statistics-R","text":"Perl interface with the R statistical program
homepage: https://metacpan.org/pod/Statistics::R
version toolchain 0.34 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/Strainberry/","title":"Strainberry","text":"Strainberry is a method that performs strain separation in low-complexity metagenomes using error-prone long-read technologies. It exploits state-of-the-art tools for variant calling, haplotype phasing, and genome assembly, in order to achieve single-sample assembly of strains with higher quality than other state-of-the-art long-read assemblers.
homepage: https://github.com/rvicedomini/strainberry
version toolchain 1.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/StringTie/","title":"StringTie","text":"StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
homepage: http://ccb.jhu.edu/software/stringtie/
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","boost":0.5},{"location":"version-specific/supported-software/s/Structure/","title":"Structure","text":"The program structure is a free software package for using multi-locus genotype data to investigate population structure.
homepage: https://web.stanford.edu/group/pritchardlab/structure.html
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","boost":0.5},{"location":"version-specific/supported-software/s/Structure_threader/","title":"Structure_threader","text":"A program to parallelize the runs of Structure, fastStructure, MavericK and ALStructure software.
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","boost":0.5},{"location":"version-specific/supported-software/s/Subread/","title":"Subread","text":"High performance read alignment, quantification and mutation discovery
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","boost":0.5},{"location":"version-specific/supported-software/s/Subversion/","title":"Subversion","text":"Subversion is an open source version control system.
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","boost":0.5},{"location":"version-specific/supported-software/s/simint/","title":"simint","text":"Simint is a vectorized implementation of the Obara-Saika (OS) method of calculating electron repulsion integrals. Speedup is gained by vectorizing the primitive loop of the OS algorithm, with additional vectorization and optimizations left to the compiler.
homepage: https://www.bennyp.org/research/simint/
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","boost":0.5},{"location":"version-specific/supported-software/s/simpy/","title":"simpy","text":"SimPy is a process-based discrete-event simulation framework based on standard Python.
homepage: https://simpy.readthedocs.io
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","boost":0.5},{"location":"version-specific/supported-software/s/sinto/","title":"sinto","text":"Sinto is a toolkit for processing aligned single-cell data.
homepage: https://timoast.github.io/sinto/index.html
version toolchain 0.7.4 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/sirocco/","title":"sirocco","text":"C++ library that allows to compute piecewise linear approximations of the path followed by the root of a complex polynomial
homepage: https://github.com/miguelmarco/SIROCCO2/
version toolchain 2.1.0 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/siscone/","title":"siscone","text":"Hadron Seedless Infrared-Safe Cone jet algorithm
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version toolchain 3.0.5 GCCcore/11.3.0 3.0.6 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/sketchmap/","title":"sketchmap","text":"Sketch-map is a dimensionality reduction algorithm that is particularly well suited to examining the high-dimensionality data that is routinely produced in atomistic simulations.
homepage: http://sketchmap.org/
version toolchain 20170130 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/skewer/","title":"skewer","text":"skewer implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.
homepage: https://github.com/relipmoc/skewer
version toolchain 0.2.2 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/sklearn-pandas/","title":"sklearn-pandas","text":"This module provides a bridge between Scikit-Learn's machine learning methods and pandas-style Data Frames. In particular, it provides a way to map DataFrame columns to transformations, which are later recombined into features.
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version toolchain 2.2.0 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/sklearn-som/","title":"sklearn-som","text":"A simple, planar self-organizing map with methods similar to clustering methods in Scikit Learn.
homepage: https://github.com/rileypsmith/sklearn-som
version toolchain 1.1.0 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/skorch/","title":"skorch","text":"A scikit-learn compatible neural network library that wraps PyTorch.
homepage: https://skorch.readthedocs.io/
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","boost":0.5},{"location":"version-specific/supported-software/s/sktime/","title":"sktime","text":"sktime is a library for time series analysis in Python. It provides a unified interface for multiple time series learning tasks. Currently, this includes time series classification, regression, clustering, annotation, and forecasting. It comes with time series algorithms and scikit-learn compatible tools to build, tune and validate time series models.
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","boost":0.5},{"location":"version-specific/supported-software/s/slepc4py/","title":"slepc4py","text":"Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations.
homepage: https://bitbucket.org/slepc/slepc4py
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","boost":0.5},{"location":"version-specific/supported-software/s/sleuth/","title":"sleuth","text":"Investigate RNA-Seq transcript abundance from kallisto and perform differential expression analysis.
homepage: http://pachterlab.github.io/sleuth
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","boost":0.5},{"location":"version-specific/supported-software/s/slidingwindow/","title":"slidingwindow","text":"slidingwindow is a simple little Python library for computing a set of windows into a larger dataset, designed for use with image-processing algorithms that utilise a sliding window to break the processing up into a series of smaller chunks.
homepage: https://github.com/adamrehn/slidingwindow
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","boost":0.5},{"location":"version-specific/supported-software/s/slow5tools/","title":"slow5tools","text":"slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.
homepage: https://hasindu2008.github.io/slow5tools
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","boost":0.5},{"location":"version-specific/supported-software/s/slurm-drmaa/","title":"slurm-drmaa","text":"DRMAA for Slurm Workload Manager (Slurm) is an implementation of Open Grid Forum Distributed Resource Management Application API (DRMAA) version 1 for submission and control of jobs to Slurm. Using DRMAA, grid applications builders, portal developers and ISVs can use the same high-level API to link their software with different cluster/resource management systems.
homepage: https://github.com/natefoo/slurm-drmaa
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","boost":0.5},{"location":"version-specific/supported-software/s/smafa/","title":"smafa","text":"Smafa attempts to align or cluster pre-aligned biological sequences, handling sequences which are all the same length.
homepage: https://github.com/wwood/smafa
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","boost":0.5},{"location":"version-specific/supported-software/s/smallgenomeutilities/","title":"smallgenomeutilities","text":"The smallgenomeutilities are a collection of scripts that is useful for dealing and manipulating NGS data of small viral genomes. They are written in Python 3 with a small number of dependencies.
homepage: https://github.com/cbg-ethz/smallgenomeutilities
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","boost":0.5},{"location":"version-specific/supported-software/s/smfishHmrf/","title":"smfishHmrf","text":"smFish spatial pattern mining and cell type prediction
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","boost":0.5},{"location":"version-specific/supported-software/s/smithwaterman/","title":"smithwaterman","text":"smith-waterman-gotoh alignment algorithm.
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","boost":0.5},{"location":"version-specific/supported-software/s/smooth-topk/","title":"smooth-topk","text":"Smooth Loss Functions for Deep Top-k Classification
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","boost":0.5},{"location":"version-specific/supported-software/s/snakemake/","title":"snakemake","text":"The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
homepage: https://snakemake.readthedocs.io
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","boost":0.5},{"location":"version-specific/supported-software/s/snaphu/","title":"snaphu","text":"SNAPHU is an implementation of the Statistical-cost, Network-flow Algorithm for Phase Unwrapping proposed by Chen and Zebker
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","boost":0.5},{"location":"version-specific/supported-software/s/snappy/","title":"snappy","text":"Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.
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","boost":0.5},{"location":"version-specific/supported-software/s/snippy/","title":"snippy","text":"Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). Rapid haploid variant calling and core genome alignment.
homepage: https://github.com/tseemann/snippy
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homepage: http://sourceforge.net/projects/snpeff/
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homepage: https://github.com/espeak-ng/sonic
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","boost":0.5},{"location":"version-specific/supported-software/s/speech_tools/","title":"speech_tools","text":"The Edinburgh Speech Tools Library is a collection of C++ class, functions and related programs for manipulating the sorts of objects used in speech processing. It includes support for reading and writing waveforms, parameter files (LPC, Ceptra, F0) in various formats and converting between them. It also includes support for linguistic type objects and support for various label files and ngrams (with smoothing).
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homepage: https://github.com/danielegrattarola/spektral
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","boost":0.5},{"location":"version-specific/supported-software/s/spglib-python/","title":"spglib-python","text":"Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.
homepage: https://pypi.python.org/pypi/spglib
version versionsuffix toolchain 1.10.0.2 -Python-2.7.14 intel/2017b 1.10.0.2 -Python-3.6.3 intel/2017b 1.14.1.post0 -Python-3.7.2 intel/2019a 1.16.0 -Python-3.8.2 foss/2020a 1.16.0 foss/2020b 1.16.0 -Python-3.7.4 fosscuda/2019b 1.16.0 fosscuda/2020b 1.16.0 -Python-3.7.4 intel/2019b 1.16.0 -Python-3.8.2 intel/2020a 1.16.0 intel/2020b 1.16.0 -Python-3.7.4 intelcuda/2019b 1.16.1 foss/2021a 1.16.1 gomkl/2021a 1.16.1 intel/2021a 1.16.3 foss/2021b 1.16.3 intel/2021b 1.9.4.2 -Python-2.7.12 intel/2016b 1.9.5 -Python-2.7.12 intel/2016b 1.9.9.38 -Python-2.7.13 intel/2017a 2.0.0 foss/2022a 2.0.0 intel/2022a 2.0.2 gfbf/2022b 2.1.0 gfbf/2023a 2.1.0 iimkl/2023a 2.5.0 gfbf/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/spglib/","title":"spglib","text":"Spglib is a C library for finding and handling crystal symmetries.
homepage: https://spglib.github.io/spglib/
version toolchain 1.16.1 GCCcore/10.2.0 1.16.2 GCCcore/10.3.0 1.9.2 intel/2016.02-GCC-4.9 1.9.9 intel/2017b 2.0.2 GCCcore/11.3.0 2.0.2 GCCcore/12.2.0 2.5.0 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/spla/","title":"spla","text":"SPLA provides specialized functions for linear algebra computations with a C++ and C interface, which are inspired by requirements in computational material science codes.
homepage: https://github.com/eth-cscs/spla/
version toolchain 1.6.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/split-seq/","title":"split-seq","text":"Analysis tools for split-seq.
homepage: https://github.com/yjzhang/split-seq-pipeline
version versionsuffix toolchain 20190717 -Python-3.6.6 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/splitRef/","title":"splitRef","text":"splitRef splits a reference haplotype file into smaller files with subsets of markers. The current version is a pre-release.
homepage: http://www.sph.umich.edu/csg/yli/splitRef/index.html
version toolchain 0.0.2 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/spoa/","title":"spoa","text":"Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences
homepage: https://github.com/rvaser/spoa
version toolchain 3.0.1 GCC/7.3.0-2.30 3.4.0 GCC/10.2.0 4.0.0 GCC/8.3.0 4.0.7 GCC/10.2.0 4.0.7 GCC/10.3.0 4.0.7 GCC/11.2.0 4.0.7 GCC/11.3.0 4.0.7 GCC/12.2.0 4.1.0 GCC/12.3.0 4.1.0 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/sradownloader/","title":"sradownloader","text":"SRAdownloader takes the annotation table from the SRA run selector tool and retrieves the raw fastq files for the selected samples
homepage: https://github.com/s-andrews/sradownloader
version toolchain 3.9 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/stardist/","title":"stardist","text":"Object Detection with Star-convex Shapes.
homepage: https://github.com/stardist/stardist
version versionsuffix toolchain 0.8.3 -CUDA-11.4.1 foss/2021b 0.8.3 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/starparser/","title":"starparser","text":"Use this package to manipulate Relion star files, including counting, modifying, plotting, and sifting the data. At the very least, this is a useful alternative to awk commands, which can get awkward. Below is a description of the command- line options with some examples. Alternatively, use starparser within Relion or load the modules in your own Python scripts.
homepage: https://github.com/sami-chaaban/starparser
version toolchain 1.49 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/stars/","title":"stars","text":"Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in R, using GDAL bindings provided by sf, and NetCDF bindings by ncmeta and RNetCDF.
homepage: https://cran.r-project.org/package=stars
version versionsuffix toolchain 0.4-3 -R-4.0.0-Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/statsmodels/","title":"statsmodels","text":"Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests.
homepage: http://statsmodels.sourceforge.net/
version versionsuffix toolchain 0.10.1 foss/2019a 0.11.0 -Python-3.7.4 foss/2019b 0.11.0 -Python-3.7.4 intel/2019b 0.11.1 -Python-3.8.2 foss/2020a 0.11.1 -Python-3.8.2 intel/2020a 0.12.1 foss/2020b 0.12.1 fosscuda/2020b 0.12.1 intel/2020b 0.12.2 foss/2021a 0.13.1 foss/2021b 0.13.1 foss/2022a 0.13.1 intel/2021b 0.14.0 gfbf/2022b 0.14.1 gfbf/2023a 0.14.1 gfbf/2023b 0.6.1 -Python-2.7.13 foss/2017a 0.6.1 -Python-3.5.1 intel/2016a 0.6.1 -Python-3.5.2 intel/2016b 0.8.0 -Python-2.7.13 intel/2017a 0.9.0 -Python-2.7.15 foss/2018b 0.9.0 -Python-3.6.6 foss/2018b 0.9.0 -Python-2.7.15 intel/2018b 0.9.0 -Python-3.6.6 intel/2018b 0.9.0 -Python-2.7.16 intel/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/stpipeline/","title":"stpipeline","text":"The ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format to generated datasets for down-stream analysis. The ST pipeline can also be used to process single cell data as long as a file with barcodes identifying each cell is provided. The ST Pipeline can also process RNA-Seq datasets generated with or without UMIs.
homepage: https://github.com/SpatialTranscriptomicsResearch/st_pipeline
version versionsuffix toolchain 1.7.3 -Python-2.7.15 foss/2018b 1.7.6 -Python-3.7.2 foss/2019a 1.7.6 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/strace/","title":"strace","text":"strace is a diagnostic, debugging and instructional userspace utility for Linux. It is used to monitor and tamper with interactions between processes and the Linux kernel, which include system calls, signal deliveries, and changes of process state.
homepage: https://strace.io/
version toolchain 5.14 GCCcore/11.2.0 6.6 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/strelka/","title":"strelka","text":"Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.
homepage: https://github.com/Illumina/strelka
version versionsuffix toolchain 2.9.10 -Python-2.7.15 foss/2018b 2.9.10 -Python-2.7.15 intel/2018b 2.9.7 intel/2018a 2.9.9 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/stripy/","title":"stripy","text":"A Python interface to TRIPACK and STRIPACK Fortran code for (constrained) triangulation in Cartesian coordinates and on a sphere. Stripy is an object-oriented package and includes routines from SRFPACK and SSRFPACK for interpolation (nearest neighbor, linear and hermite cubic) and to evaluate derivatives (Renka 1996a,b and 1997a,b).
homepage: https://github.com/underworldcode/stripy
version toolchain 2.1.0 foss/2021a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/suave/","title":"suave","text":"suave is an interactive web application to visualize read depth ratios between two samples and the structural variants of one of the samples (typically the \"case\" sample in a case/control setup such as tumor/normal comparison).
homepage: https://github.com/dellytools/suave
version toolchain 20160529 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/submitit/","title":"submitit","text":"Submitit is a lightweight tool for submitting Python functions for computation within a Slurm cluster.
homepage: https://github.com/facebookincubator/submitit
version toolchain 1.2.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/subset-bam/","title":"subset-bam","text":"subset-bam is a tool to subset a 10x Genomics BAM file based on a tag, most commonly the cell barcode tag.
homepage: https://github.com/10XGenomics/subset-bam
version toolchain 1.1.0 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/subunit/","title":"subunit","text":"Subunit is a streaming protocol for test results.
homepage: https://github.com/testing-cabal/subunit
version toolchain 1.4.3 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/suds/","title":"suds","text":"Lightweight SOAP client
homepage: https://pypi.python.org/pypi/suds-py3
version versionsuffix toolchain 1.3.3.0 -Python-3.6.4 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/supermagic/","title":"supermagic","text":"Very simple MPI sanity code. Nothing more, nothing less.
homepage: https://github.com/hpc/supermagic
version toolchain 20170824 foss/2017a 20170824 gompi/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/supernova/","title":"supernova","text":"Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source
homepage: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome
version toolchain 2.0.1 system 2.1.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/svist4get/","title":"svist4get","text":"Svist4get is a simple bioinformatics tool for visualization of genomic signal tracks in user-defined genomic windows, either arbitrary selected by genomic coordinates or anchored to particular transcripts or genes.
homepage: https://github.com/art-egorov/svist4get
version toolchain 1.3.1 foss/2020b 1.3.1 foss/2022b 1.3.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/swarm/","title":"swarm","text":"A robust and fast clustering method for amplicon-based studies
homepage: https://github.com/torognes/swarm
version toolchain 2.2.2 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/swifter/","title":"swifter","text":"A package which efficiently applies any function to a pandas dataframe or series in the fastest available manner.
homepage: https://github.com/jmcarpenter2/swifter
version toolchain 1.0.9 foss/2020b 1.0.9 fosscuda/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/swissknife/","title":"swissknife","text":"Perl module for reading and writing UniProtKB data in plain text format.
homepage: https://sourceforge.net/projects/swissknife/
version toolchain 1.80 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/sympy/","title":"sympy","text":"SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.
homepage: https://sympy.org/
version versionsuffix toolchain 1.0 -Python-2.7.11 foss/2016a 1.0 -Python-2.7.11 intel/2016a 1.10.1 foss/2022a 1.10.1 intel/2022a 1.11.1 foss/2022a 1.11.1 intel/2022a 1.12 gfbf/2022b 1.12 gfbf/2023a 1.12 gfbf/2023b 1.3 -Python-2.7.15 foss/2018b 1.3 -Python-3.6.6 foss/2018b 1.3 -Python-2.7.14 intel/2018a 1.3 -Python-3.6.4 intel/2018a 1.4 foss/2019a 1.4 intel/2019a 1.5.1 -Python-3.7.4 foss/2019b 1.6.2 -Python-3.8.2 foss/2020a 1.7.1 foss/2020b 1.7.1 intel/2020b 1.8 foss/2021a 1.9 foss/2021b 1.9 intel/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/synapseclient/","title":"synapseclient","text":"The synapseclient package provides an interface to Synapse, a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate, providing support for: integrated presentation of data, code and text fine grained access control provenance tracking The synapseclient package lets you communicate with the cloud-hosted Synapse service to access data and create shared data analysis projects from within Python scripts or at the interactive Python console. Other Synapse clients exist for R, Java, and the web. The Python client can also be used from the command line.
homepage: https://help.synapse.org/docs/
version toolchain 3.0.0 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/synthcity/","title":"synthcity","text":"A library for generating and evaluating synthetic tabular data.
homepage: https://github.com/vanderschaarlab/synthcity
version toolchain 0.2.4 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/s/sysbench/","title":"sysbench","text":"sysbench is a scriptable multi-threaded benchmark tool based on LuaJIT. It is most frequently used for database benchmarks, but can also be used to create arbitrarily complex workloads that do not involve a database server.
homepage: https://github.com/akopytov/sysbench
version toolchain 1.0.20 GCC/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/","title":"List of supported software (t)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- T-Coffee
- t-SNE-CUDA
- tabix
- tabixpp
- taco
- TagDust
- TagLib
- Taiyaki
- TALON
- TALYS
- TAMkin
- tantan
- Tapenade
- task-spooler
- taxator-tk
- TBA
- tbb
- tbl2asn
- TCC
- Tcl
- TCLAP
- tcsh
- tdlib
- tecplot360ex
- TELEMAC-MASCARET
- Telescope
- Teneto
- tensorboard
- tensorboardX
- TensorFlow
- tensorflow-compression
- TensorFlow-Datasets
- TensorFlow-Graphics
- tensorflow-probability
- TensorRT
- terastructure
- termcolor
- Tesla-Deployment-Kit
- tesseract
- testpath
- TetGen
- TEToolkit
- TEtranscripts
- texinfo
- texlive
- Text-CSV
- TF-COMB
- TFEA
- Theano
- ThemisPy
- THetA
- thirdorder
- thurstonianIRT
- TiCCutils
- tidybayes
- tidymodels
- Tika
- tiktoken
- TiMBL
- time
- timm
- TINKER
- tiny-cuda-nn
- TinyDB
- TinyXML
- Tk
- Tkinter
- TM-align
- tMAE
- tmap
- tmux
- TN93
- TOBIAS
- ToFu
- Togl
- toil
- tokenizers
- Tombo
- TOML-Fortran
- TOPAS
- topaz
- TopHat
- torch-em
- torchaudio
- torchdata
- torchinfo
- TorchIO
- torchsampler
- torchtext
- torchvf
- torchvision
- tornado
- TotalView
- tox
- tqdm
- Tracer
- TranscriptClean
- TransDecoder
- Transformers
- Transrate
- travis
- TRAVIS-Analyzer
- treatSens
- TreeMix
- TreeShrink
- TRF
- Triangle
- Trilinos
- Trim_Galore
- trimAl
- trimesh
- Trimmomatic
- Trinity
- Trinotate
- Triplexator
- TRIQS
- TRIQS-cthyb
- TRIQS-dft_tools
- TRIQS-tprf
- Triton
- tRNAscan-SE
- TRUST
- TRUST4
- Trycycler
- tseriesEntropy
- tsne
- turbinesFoam
- TurboVNC
- TVB
- tvb-data
- TVB-deps
- tvb-framework
- tvb-library
- TWL-NINJA
- TXR
- typing-extensions
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/T-Coffee/","title":"T-Coffee","text":"A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures
homepage: https://www.tcoffee.org/
version toolchain 13.45.61.3c310a9 system 13.46.0.919e8c6b system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TALON/","title":"TALON","text":"TALON is a Python package for identifying and quantifying known and novel genes/isoforms in long-read transcriptome data sets. TALON is technology-agnostic in that it works from mapped SAM files, allowing data from different sequencing platforms (i.e. PacBio and Oxford Nanopore) to be analyzed side by side.
homepage: https://github.com/mortazavilab/TALON
version toolchain 5.0 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TALYS/","title":"TALYS","text":"TALYS is a nuclear reaction program.
homepage: https://tendl.web.psi.ch/tendl_2019/talys.html
version toolchain 1.95 GCCcore/10.3.0 1.95 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TAMkin/","title":"TAMkin","text":"TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry and reaction kinetics. It uses a Hessian computation from a standard computational chemistry program as its input.
homepage: http://molmod.github.io/tamkin/
version versionsuffix toolchain 1.0.9 -Python-2.7.11 intel/2016a 1.2.4 -Python-2.7.14 intel/2017b 1.2.6 -Python-3.8.2 foss/2020a 1.2.6 foss/2020b 1.2.6 foss/2021a 1.2.6 foss/2021b 1.2.6 foss/2022a 1.2.6 foss/2022b 1.2.6 foss/2023a 1.2.6 -Python-3.7.2 intel/2019a 1.2.6 -Python-3.8.2 intel/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TBA/","title":"TBA","text":"TBA (a Transcription factor Binding Analysis): TBA is a multi-functional machine learning tool for identifying transcription factors associated with genomic features
homepage: https://github.com/jenhantao/tba
version toolchain 1.0 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TCC/","title":"TCC","text":"The Tiny C Compiler (aka TCC, tCc, or TinyCC) is an x86 and x86-64 C compiler created by Fabrice Bellard. It is designed to work for slow computers with little disk space and can run shebang style !/usr/bin/tcc . TCC is distributed under the LGPL. TCC claims to implement all of ANSI C (C89/C90),[1] much of the new ISO C99 standard, and many GNU C extensions including inline assembly.
homepage: http://bellard.org/tcc/
version toolchain 0.9.26 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TCLAP/","title":"TCLAP","text":"TCLAP is a small, flexible library that provides a simple interface for defining and accessing command line arguments. It was intially inspired by the user friendly CLAP libary.
homepage: http://tclap.sourceforge.net/
version toolchain 1.2.2 GCCcore/8.3.0 1.2.4 GCCcore/10.2.0 1.2.4 GCCcore/9.3.0 1.2.5 GCCcore/10.3.0 1.2.5 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TELEMAC-MASCARET/","title":"TELEMAC-MASCARET","text":"TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free-surface flow. Having been used in the context of many studies throughout the world, it has become one of the major standards in its field.
homepage: http://www.opentelemac.org
version toolchain 8p3r1 foss/2021b 8p5r0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TEToolkit/","title":"TEToolkit","text":"Tools for estimating differential enrichment of Transposable Elements and other highly repetitive regions
homepage: http://hammelllab.labsites.cshl.edu/software/#TEToolkit
version versionsuffix toolchain 1.5.1 -Python-2.7.11 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TEtranscripts/","title":"TEtranscripts","text":"TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates reads to both genes & transposable elements. TEtranscripts then performs differential analysis using DESeq2.
homepage: https://github.com/mhammell-laboratory/TEtranscripts
version toolchain 2.2.0 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TF-COMB/","title":"TF-COMB","text":"Transcription Factor Co-Occurrence using Market Basket analysis.
homepage: https://github.com/loosolab/TF-COMB
version toolchain 1.1 foss/2022b 1.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TFEA/","title":"TFEA","text":"Transcription Factor Enrichment Analysis
homepage: https://github.com/Dowell-Lab/TFEA
version versionsuffix toolchain 1.1.4 -muMerge-1.1.0 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/THetA/","title":"THetA","text":"Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data.
homepage: https://github.com/raphael-group/THetA
version versionsuffix toolchain 0.7 -Python-2.7.15 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TINKER/","title":"TINKER","text":"The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
homepage: http://dasher.wustl.edu/tinker
version toolchain 8.6.1 foss/2018b 8.7.2 foss/2019b 8.8.1 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TM-align/","title":"TM-align","text":"This package unifies protein structure alignment and RNA structure alignment into the standard TM-align program for single chain structure alignment, MM-align program for multi-chain structure alignment, and TM-score program for sequence dependent structure superposition.
homepage: https://zhanglab.ccmb.med.umich.edu/RNA-align/TMalign/
version toolchain 20180426 foss/2018b 20180426 intel/2019a 20190822 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TN93/","title":"TN93","text":"This is a simple program meant to compute pairwise distances between aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance.
homepage: https://github.com/veg/tn93
version toolchain 1.0.7 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TOBIAS/","title":"TOBIAS","text":"TOBIAS is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data, and includes: Correction of Tn5 insertion bias; Calculation of footprint scores within regulatory regions; Estimation of bound/unbound transcription factor binding sites; and Visualization of footprints within and across different conditions
homepage: https://github.com/loosolab/TOBIAS
version toolchain 0.12.12 foss/2021b 0.14.0 foss/2020b 0.16.1 foss/2022b 0.16.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TOML-Fortran/","title":"TOML-Fortran","text":"TOML parser for Fortran projects
homepage: https://github.com/toml-f/toml-f
version toolchain 0.2.2 GCC/10.2.0 0.2.2 iccifort/2020.4.304 0.3.1 GCC/11.2.0 0.3.1 GCC/11.3.0 0.4.1 GCC/12.2.0 0.4.1 intel-compilers/2022.2.1 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TOPAS/","title":"TOPAS","text":"TOPAS wraps and extends the Geant4 Simulation Toolkit to make advanced Monte Carlo simulation of all forms of radiotherapy easier to use for medical physicists.
homepage: https://www.topasmc.org
version toolchain 3.9 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TRAVIS-Analyzer/","title":"TRAVIS-Analyzer","text":"TRAVIS is a free tool for analyzing and visualizing trajectories from all kinds of Molecular Dynamics or Monte Carlo simulations.
homepage: http://www.travis-analyzer.de/
version toolchain 210521 GCC/10.3.0 220729 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TRF/","title":"TRF","text":"Tandem repeats finder: a program to analyze DNA sequences. Legacy version.
homepage: https://tandem.bu.edu/trf/trf.html
version versionsuffix toolchain 4.09 -linux64 system 4.09.1 GCC/10.3.0 4.09.1 GCCcore/10.2.0 4.09.1 GCCcore/11.2.0 4.09.1 GCCcore/11.3.0 4.09.1 GCCcore/12.3.0 4.09.1 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TRIQS-cthyb/","title":"TRIQS-cthyb","text":"TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. cthyb = continuous-time hybridisation-expansion quantum Monte Carlo The TRIQS-based hybridization-expansion solver allows to solve the generic problem of a quantum impurity embedded in a conduction bath for an arbitrary local interaction vertex. The \u201cimpurity\u201d can be any set of orbitals, on one or several atoms.
homepage: https://triqs.github.io/cthyb/
version versionsuffix toolchain 2.2.0 -Python-2.7.15 foss/2019a 3.0.0 -Python-3.8.2 foss/2020a 3.1.0 foss/2022a 3.2.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TRIQS-dft_tools/","title":"TRIQS-dft_tools","text":"TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. This TRIQS-based-based application is aimed at ab-initio calculations for correlated materials, combining realistic DFT band-structure calculations with the dynamical mean-field theory. Together with the necessary tools to perform the DMFT self-consistency loop for realistic multi-band problems, the package provides a full-fledged charge self-consistent interface to the Wien2K package. In addition, if Wien2k is not available, it provides a generic interface for one-shot DFT+DMFT calculations, where only the single-particle Hamiltonian in orbital space has to be provided.
homepage: https://triqs.github.io/dft_tools
version versionsuffix toolchain 2.2.0 -Python-2.7.15 foss/2019a 3.0.0 -Python-3.8.2 foss/2020a 3.1.0 foss/2022a 3.2.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TRIQS-tprf/","title":"TRIQS-tprf","text":"TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. TPRF is a TRIQS-based two-particle response function tool box that implements basic operations for higher order response functions such as inversion, products, the random phase approximation, the bethe salpeter equation (in the local vertex approximation), etc.. The aim is to provide efficient (C++/OpenMP/MPI) implementations of the basic operations needed to compute the two-particle response in the different two-particle channels (particle-hole, particle-particle).
homepage: https://triqs.github.io/tprf
version versionsuffix toolchain 2.2.0 -Python-2.7.15 foss/2019a 3.0.0 -Python-3.8.2 foss/2020a 3.1.1 foss/2022a 3.2.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TRIQS/","title":"TRIQS","text":"TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems.
homepage: https://triqs.github.io/
version versionsuffix toolchain 2.2.0 -Python-2.7.15 foss/2019a 2.2.1 -Python-2.7.15 foss/2019a 3.0.0 -Python-3.8.2 foss/2020a 3.1.1 foss/2022a 3.2.0 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TRUST/","title":"TRUST","text":"Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors.
homepage: https://bitbucket.org/liulab/trust
version versionsuffix toolchain 3.0.2 -Python-2.7.14 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TRUST4/","title":"TRUST4","text":"Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR sequences.
homepage: https://github.com/liulab-dfci/TRUST4
version toolchain 1.0.5.1 system 1.0.6 GCC/11.2.0 1.0.7 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TVB-deps/","title":"TVB-deps","text":"Bundle of dependency Python packages for TVB (The Virtual Brain)
homepage: https://thevirtualbrain.org
version versionsuffix toolchain 20160618 -Python-2.7.11 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TVB/","title":"TVB","text":"The Virtual Brain will deliver the first open simulation of the human brain based on individual large-scale connectivity.
homepage: http://thevirtualbrain.org
version versionsuffix toolchain 1.4.1 -Python-2.7.11 intel/2016a 1.5 -Python-2.7.11 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TWL-NINJA/","title":"TWL-NINJA","text":"Nearly Infinite Neighbor Joining Application.
homepage: https://github.com/TravisWheelerLab/NINJA
version toolchain 0.97-cluster_only GCC/10.2.0 0.98-cluster_only GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TXR/","title":"TXR","text":"TXR is a pragmatic, convenient tool ready to take on your daily hacking challenges with its dual personality: its whole-document pattern matching and extraction language for scraping information from arbitrary text sources, and its powerful data-processing language to slice through problems like a hot knife through butter. Many tasks can be accomplished with TXR \"one liners\" directly from your system prompt.
homepage: https://www.nongnu.org/txr/
version toolchain 291 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TagDust/","title":"TagDust","text":"Raw sequences produced by next generation sequencing (NGS) machines may contain adapter, linker, barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the sequences to be mapped in downstream pipelines.
homepage: http://tagdust.sourceforge.net/
version toolchain 2.33 GCCcore/10.2.0 2.33 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TagLib/","title":"TagLib","text":"TagLib is a library for reading and editing the meta-data of several popular audio formats.
homepage: https://taglib.org/
version toolchain 1.11.1 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/Taiyaki/","title":"Taiyaki","text":"Taiyaki is research software for training models for basecalling Oxford Nanopore reads.
homepage: https://github.com/nanoporetech/taiyaki
version versionsuffix toolchain 5.1.0-20200617 -Python-3.7.2-PyTorch-1.2.0 foss/2019a 5.1.0-20200617 -Python-3.7.2-PyTorch-1.2.0 fosscuda/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/Tapenade/","title":"Tapenade","text":"Tool for Algorithmic Differentiation of programs.
homepage: https://tapenade.gitlabpages.inria.fr/tapenade/docs/html/index.html
version versionsuffix toolchain 3.16 -Java-17 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/Tcl/","title":"Tcl","text":"Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.
homepage: http://www.tcl.tk/
version toolchain 8.5.19 foss/2017a 8.6.10 GCCcore/10.2.0 8.6.10 GCCcore/9.3.0 8.6.11 GCCcore/10.3.0 8.6.11 GCCcore/11.2.0 8.6.12 GCCcore/11.3.0 8.6.12 GCCcore/12.2.0 8.6.13 GCCcore/12.3.0 8.6.13 GCCcore/13.1.0 8.6.13 GCCcore/13.2.0 8.6.14 GCCcore/13.3.0 8.6.3 GCC/4.8.4 8.6.3 GCC/4.9.2 8.6.4 GCC/4.9.3-2.25 8.6.4 GNU/4.9.3-2.25 8.6.4 foss/2016a 8.6.4 gimkl/2.11.5 8.6.4 intel/2016.02-GCC-4.9 8.6.4 intel/2016a 8.6.4 iomkl/2016.07 8.6.4 iomkl/2016.09-GCC-4.9.3-2.25 8.6.5 GCC/4.9.3-2.25 8.6.5 GCC/5.4.0-2.26 8.6.5 GCCcore/6.3.0 8.6.5 foss/2016.04 8.6.5 foss/2016a 8.6.5 foss/2016b 8.6.5 iccifort/2016.3.210-GCC-5.4.0-2.26 8.6.5 intel/2016b 8.6.6 GCCcore/4.9.3 8.6.6 GCCcore/6.3.0 8.6.7 GCCcore/6.4.0 8.6.8 GCCcore/6.4.0 8.6.8 GCCcore/7.2.0 8.6.8 GCCcore/7.3.0 8.6.9 GCCcore/8.2.0 8.6.9 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/Telescope/","title":"Telescope","text":"Single locus resolution of Transposable ELEment expression using next-generation sequencing.
homepage: https://github.com/mlbendall/telescope
version versionsuffix toolchain 1.0.3 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/Teneto/","title":"Teneto","text":"Teneto is package for deriving, analysing and plotting temporal network representations. Additional tools for temporal network analysis with neuroimaging contexts.
homepage: https://teneto.readthedocs.io
version versionsuffix toolchain 0.5.1 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TensorFlow-Datasets/","title":"TensorFlow-Datasets","text":"TensorFlow Datasets is a collection of datasets ready to use, with TensorFlow or other Python ML frameworks, such as Jax. All datasets are exposed as tf.data.Datasets , enabling easy-to-use and high-performance input pipelines.
homepage: https://www.tensorflow.org/datasets
version versionsuffix toolchain 4.7.0 -CUDA-11.3.1 foss/2021a 4.8.3 -CUDA-11.4.1 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TensorFlow-Graphics/","title":"TensorFlow-Graphics","text":"Tensorflow Graphics provides a set of differentiable graphics and geometry layers (e.g. cameras, reflectance models, spatial transformations, mesh convolutions) and 3D viewer functionalities (e.g. 3D TensorBoard) that can be used to train and debug your machine learning models of choice.
homepage: https://github.com/tensorflow/graphics
version versionsuffix toolchain 2021.12.3 -CUDA-11.4.1 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TensorFlow/","title":"TensorFlow","text":"An open-source software library for Machine Intelligence
homepage: https://www.tensorflow.org/
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","boost":0.5},{"location":"version-specific/supported-software/t/TensorRT/","title":"TensorRT","text":"NVIDIA TensorRT is a platform for high-performance deep learning inference
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","boost":0.5},{"location":"version-specific/supported-software/t/Tesla-Deployment-Kit/","title":"Tesla-Deployment-Kit","text":"The Tesla Deployment Kit is a set of tools provided primarily for the NVIDIA Tesla range of GPUs. They aim to empower users to better manage their NVIDIA GPUs by providing a broad range of functionalities. The kit contains: * NVIDIA Management Library (NVML), * Tesla Deployment Kit - Linux Edition (Aug 1st, 2013)
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version toolchain 5.319.43 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TetGen/","title":"TetGen","text":"A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator
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","boost":0.5},{"location":"version-specific/supported-software/t/Text-CSV/","title":"Text-CSV","text":"Text-CSV parser
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version versionsuffix toolchain 1.33 -Perl-5.22.1 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/Theano/","title":"Theano","text":"Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
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","boost":0.5},{"location":"version-specific/supported-software/t/ThemisPy/","title":"ThemisPy","text":"A header-only C++ library for L-BFGS and L-BFGS-B algorithms
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","boost":0.5},{"location":"version-specific/supported-software/t/TiCCutils/","title":"TiCCutils","text":"TiCC utils is a collection of generic C++ software which is used in a lot of programs produced at Tilburg centre for Cognition and Communication (TiCC) at Tilburg University and Centre for Dutch Language and Speech at University of Antwerp.
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","boost":0.5},{"location":"version-specific/supported-software/t/TiMBL/","title":"TiMBL","text":"TiMBL (Tilburg Memory Based Learner) is an open source software package implementing several memory-based learning algorithms, among which IB1-IG, an implementation of k-nearest neighbor classification with feature weighting suitable for symbolic feature spaces, and IGTree, a decision-tree approximation of IB1-IG. All implemented algorithms have in common that they store some representation of the training set explicitly in memory. During testing, new cases are classified by extrapolation from the most similar stored cases.
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","boost":0.5},{"location":"version-specific/supported-software/t/Tika/","title":"Tika","text":"The Apache Tika toolkit detects and extracts metadata and text from over a thousand different file types (such as PPT, XLS, and PDF).
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version toolchain 1.16 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TinyDB/","title":"TinyDB","text":"TinyDB is a lightweight document oriented database optimized for your happiness :) It's written in pure Python and has no external dependencies. The target are small apps that would be blown away by a SQL-DB or an external database server.
homepage: https://tinydb.readthedocs.io/
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","boost":0.5},{"location":"version-specific/supported-software/t/TinyXML/","title":"TinyXML","text":"TinyXML is a simple, small, minimal, C++ XML parser that can be easily integrating into other programs. It reads XML and creates C++ objects representing the XML document. The objects can be manipulated, changed, and saved again as XML.
homepage: https://sourceforge.net/projects/tinyxml
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","boost":0.5},{"location":"version-specific/supported-software/t/Tk/","title":"Tk","text":"Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.
homepage: https://www.tcl.tk/
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","boost":0.5},{"location":"version-specific/supported-software/t/Tkinter/","title":"Tkinter","text":"Tkinter module, built with the Python buildsystem
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","boost":0.5},{"location":"version-specific/supported-software/t/ToFu/","title":"ToFu","text":"Tomography for Fusion.
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","boost":0.5},{"location":"version-specific/supported-software/t/Togl/","title":"Togl","text":"A Tcl/Tk widget for OpenGL rendering.
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homepage: https://torchio.readthedocs.io/
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","boost":0.5},{"location":"version-specific/supported-software/t/TotalView/","title":"TotalView","text":"TotalView is a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables. It allows you to debug one or many processes and/or threads in a single window with complete control over program execution. This allows you to set breakpoints, stepping line by line through the code on a single thread, or with coordinated groups of processes or threads, and run or halt arbitrary sets of processes or threads. You can reproduce and troubleshoot difficult problems that can occur in concurrent programs that take advantage of threads, OpenMP, MPI, GPUs or coprocessors.
homepage: http://www.roguewave.com/products/totalview.aspx
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","boost":0.5},{"location":"version-specific/supported-software/t/Tracer/","title":"Tracer","text":"Tracer is a graphical tool for visualization and diagnostics of MCMC output.
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version toolchain 1.7.1 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/t/TransDecoder/","title":"TransDecoder","text":"TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
homepage: https://github.com/TransDecoder/TransDecoder/wiki
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","boost":0.5},{"location":"version-specific/supported-software/t/TranscriptClean/","title":"TranscriptClean","text":"TranscriptClean is a Python program that corrects mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome.
homepage: https://github.com/mortazavilab/TranscriptClean
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","boost":0.5},{"location":"version-specific/supported-software/t/Transformers/","title":"Transformers","text":"State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0
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","boost":0.5},{"location":"version-specific/supported-software/t/Transrate/","title":"Transrate","text":"Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.
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homepage: https://www.cs.cmu.edu/~quake/triangle.html
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homepage: https://trilinos.org
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","boost":0.5},{"location":"version-specific/supported-software/t/Trim_Galore/","title":"Trim_Galore","text":"A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
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homepage: http://www.usadellab.org/cms/?page=trimmomatic
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homepage: https://trinityrnaseq.github.io
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homepage: https://triton-lang.org/
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homepage: https://tmap.gdb.tools
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","boost":0.5},{"location":"version-specific/supported-software/t/tvb-library/","title":"tvb-library","text":"The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. TVB Scientific Library is the most important scientific contribution of TVB Project.
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- UCC
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- UCX-CUDA
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- UQTk
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- UShER
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- util-linux
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/UCC-CUDA/","title":"UCC-CUDA","text":"UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. This module adds the UCC CUDA support.
homepage: https://www.openucx.org/
version versionsuffix toolchain 1.0.0 -CUDA-11.7.0 GCCcore/11.3.0 1.1.0 -CUDA-12.0.0 GCCcore/12.2.0 1.2.0 -CUDA-12.1.1 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/UCC/","title":"UCC","text":"UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes.
homepage: https://www.openucx.org/
version toolchain 1.0.0 GCCcore/11.3.0 1.1.0 GCCcore/12.2.0 1.2.0 GCCcore/12.3.0 1.2.0 GCCcore/13.2.0 1.3.0 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/UCLUST/","title":"UCLUST","text":"UCLUST: Extreme high-speed sequence clustering, alignment and database search.
homepage: https://www.drive5.com/usearch/index.html
version versionsuffix toolchain 1.2.22q -i86linux64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/UCX-CUDA/","title":"UCX-CUDA","text":"Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support.
homepage: http://www.openucx.org/
version versionsuffix toolchain 1.10.0 -CUDA-11.3.1 GCCcore/10.3.0 1.11.0 -CUDA-11.4.1 GCCcore/11.2.0 1.11.2 -CUDA-11.4.1 GCCcore/11.2.0 1.11.2 -CUDA-11.5.2 GCCcore/11.2.0 1.12.1 -CUDA-11.7.0 GCCcore/11.3.0 1.13.1 -CUDA-11.7.0 GCCcore/12.2.0 1.13.1 -CUDA-12.0.0 GCCcore/12.2.0 1.14.1 -CUDA-12.1.1 GCCcore/12.3.0 1.15.0 -CUDA-12.4.0 GCCcore/13.2.0 1.15.0 -CUDA-12.5.0 GCCcore/13.2.0 1.16.0 -CUDA-12.6.0 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/UCX-ROCm/","title":"UCX-ROCm","text":"Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX ROCm support.
homepage: http://www.openucx.org/
version versionsuffix toolchain 1.11.2 -ROCm-4.5.0 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/UCX/","title":"UCX","text":"Unified Communication X An open-source production grade communication framework for data centric and high-performance applications
homepage: https://www.openucx.org/
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","boost":0.5},{"location":"version-specific/supported-software/u/UDUNITS/","title":"UDUNITS","text":"UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
homepage: https://www.unidata.ucar.edu/software/udunits/
version toolchain 2.2.20 foss/2016a 2.2.20 intel/2016b 2.2.24 intel/2017a 2.2.25 foss/2017b 2.2.25 intel/2017b 2.2.26 GCCcore/10.2.0 2.2.26 GCCcore/8.2.0 2.2.26 GCCcore/8.3.0 2.2.26 GCCcore/9.3.0 2.2.26 foss/2018a 2.2.26 foss/2018b 2.2.26 foss/2020a 2.2.26 intel/2017b 2.2.26 intel/2018a 2.2.26 intel/2018b 2.2.26 iomkl/2018b 2.2.28 GCCcore/10.3.0 2.2.28 GCCcore/11.2.0 2.2.28 GCCcore/11.3.0 2.2.28 GCCcore/12.2.0 2.2.28 GCCcore/12.3.0 2.2.28 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/UFL/","title":"UFL","text":"The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions for weak forms in a notation close to mathematical notation.
homepage: https://bitbucket.org/fenics-project/ufl
version versionsuffix toolchain 2018.1.0 -Python-3.6.4 foss/2018a 2019.1.0 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/UMI-tools/","title":"UMI-tools","text":"Tools for handling Unique Molecular Identifiers in NGS data sets
homepage: https://umi-tools.readthedocs.io
version versionsuffix toolchain 1.0.0 -Python-3.6.6 foss/2018b 1.0.1 -Python-3.7.4 foss/2019b 1.0.1 -Python-3.8.2 foss/2020a 1.1.4 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/UNAFold/","title":"UNAFold","text":"The UNAFold package contains several programs for performing energy minimization and partition function calculations on nucleic acid sequences.
homepage: http://mfold.rna.albany.edu/?q=DINAMelt/software
version versionsuffix toolchain 3.8 -Perl-5.24.1 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/UQTk/","title":"UQTk","text":"The UQ Toolkit (UQTk) is a collection of libraries and tools for the quantification of uncertainty in numerical model predictions.
homepage: https://www.sandia.gov/UQToolkit/
version versionsuffix toolchain 3.1.0 -Python-3.7.4 intel/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/USEARCH/","title":"USEARCH","text":"USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
homepage: https://www.drive5.com/usearch/index.html
version versionsuffix toolchain 11.0.667 -i86linux32 system 5.2.236-6.1.544 -i86linux32 system 5.2.236 -i86linux32 system 6.1.544 -i86linux32 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/USPEX/","title":"USPEX","text":"USPEX (Universal Structure Predictor: Evolutionary Xtallography... and in Russian \"uspekh\" means \"success\" - owing to the high success rate and many useful results produced by this method) is a method developed by the Oganov laboratory since 2004. The problem of crystal structure prediction is very old and does, in fact, constitute the central problem of theoretical crystal chemistry. USPEX can also be used for finding low-energy metastable phases, as well as stable structures of nanoparticles, surface reconstructions, molecular packings in organic crystals, and for searching for materials with desired physical (mechanical, electronic) properties. The USPEX code is based on an efficient evolutionary algorithm developed by A.R. Oganov's group, but also has options for using alternative methods (random sampling, metadynamics, corrected particle swarm optimization algorithms). USPEX is interfaced with many ab initio codes, such as VASP, SIESTA, GULP, Quantum Espresso, CP2K, CASTEP, LAMMPS, and so on.
homepage: http://uspex-team.org/uspex/overview
version versionsuffix toolchain 9.4.4 -Python-2.7.12 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/UShER/","title":"UShER","text":"UShER is now a package consisting of a family of programs for rapid phylogenetic analyses, particularly suitable for the SARS-CoV-2 genomes.
homepage: https://github.com/yatisht/usher
version toolchain 0.4.1 gompi/2020b 0.5.0 gompi/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/Ultralytics/","title":"Ultralytics","text":"Ultralytics YOLOv8 is a cutting-edge, state-of-the-art (SOTA) model that builds upon the success of previous YOLO versions and introduces new features and improvements to further boost performance and flexibility. YOLOv8 is designed to be fast, accurate, and easy to use, making it an excellent choice for a wide range of object detection and tracking, instance segmentation, image classification and pose estimation tasks.
homepage: https://github.com/ultralytics/ultralytics
version versionsuffix toolchain 8.0.92 -CUDA-11.7.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/Umpire/","title":"Umpire","text":"Umpire is a resource management library that allows the discovery, provision, and management of memory on machines with multiple memory devices like NUMA and GPUs.
homepage: https://github.com/LLNL/Umpire
version toolchain 2024.02.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/UnZip/","title":"UnZip","text":"UnZip is an extraction utility for archives compressed in .zip format (also called \"zipfiles\"). Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own Zip program, our primary objectives have been portability and non-MSDOS functionality.
homepage: http://www.info-zip.org/UnZip.html
version toolchain 6.0 GCCcore/10.2.0 6.0 GCCcore/10.3.0 6.0 GCCcore/11.2.0 6.0 GCCcore/11.3.0 6.0 GCCcore/12.2.0 6.0 GCCcore/12.3.0 6.0 GCCcore/13.1.0 6.0 GCCcore/13.2.0 6.0 GCCcore/13.3.0 6.0 GCCcore/6.4.0 6.0 GCCcore/7.3.0 6.0 GCCcore/8.2.0 6.0 GCCcore/8.3.0 6.0 GCCcore/9.3.0 6.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/Uni-Core/","title":"Uni-Core","text":"An efficient distributed PyTorch framework
homepage: https://github.com/dptech-corp/Uni-Core
version versionsuffix toolchain 0.0.3 -CUDA-11.7.0 foss/2022a 0.0.3 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/UniFrac/","title":"UniFrac","text":"UniFrac is the de facto repository for high-performance phylogenetic diversity calculations. The methods in this repository are based on an implementation of the Strided State UniFrac algorithm which is faster, and uses less memory than Fast UniFrac. Strided State UniFrac supports Unweighted UniFrac, Weighted UniFrac, Generalized UniFrac, Variance Adjusted UniFrac and meta UniFrac, in both double and single precision (fp32). This repository also includes Stacked Faith (manuscript in preparation), a method for calculating Faith's PD that is faster and uses less memory than the Fast UniFrac-based reference implementation.
homepage: https://github.com/biocore/unifrac-binaries
version toolchain 1.3.2 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/Unicycler/","title":"Unicycler","text":"Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline.
homepage: https://github.com/rrwick/Unicycler
version versionsuffix toolchain 0.4.7 -Python-3.7.2 foss/2019a 0.4.8 -Python-3.8.2 gompi/2020a 0.4.9 gompi/2021a 0.5.0 gompi/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/Unidecode/","title":"Unidecode","text":"Python library for lossy ASCII transliterations of Unicode text (port of Text::Unidecode Perl module)
homepage: https://github.com/avian2/unidecode
version versionsuffix toolchain 1.1.1 -Python-3.7.4 GCCcore/8.3.0 1.3.6 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/ucx-py/","title":"ucx-py","text":"UCX-Py is the Python interface for UCX, a low-level high-performance networking library. UCX and UCX-Py supports several transport methods including InfiniBand and NVLink while still using traditional networking protocols like TCP.
homepage: https://ucx-py.readthedocs.io
version toolchain 0.21.0 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/udocker/","title":"udocker","text":"A basic user tool to execute simple docker containers in batch or interactive systems without root privileges.
homepage: https://github.com/indigo-dc/udocker
version versionsuffix toolchain 1.1.1 -Python-2.7.14 foss/2017b 1.1.3 -Python-2.7.14 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/umap-learn/","title":"umap-learn","text":"Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction.
homepage: https://pypi.org/project/umap-learn/
version toolchain 0.4.6 foss/2020b 0.4.6 fosscuda/2020b 0.5.3 foss/2020b 0.5.3 foss/2021a 0.5.3 foss/2021b 0.5.3 foss/2022a 0.5.5 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/umi4cPackage/","title":"umi4cPackage","text":"umi4cPackage is a processing and analysis pipeline for UMI-4C experiment.
homepage: https://github.com/tanaylab/umi4cpackage
version versionsuffix toolchain 20200116 -R-4.0.0 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/umis/","title":"umis","text":"Package for estimating UMI counts in Transcript Tag Counting data.
homepage: https://github.com/vals/umis
version toolchain 1.0.3 intel/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/uncertainties/","title":"uncertainties","text":"Transparent calculations with uncertainties on the quantities involved (aka error propagation); fast calculation of derivatives
homepage: http://uncertainties-python-package.readthedocs.io
version toolchain 3.1.7 foss/2021b 3.1.7 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/uncertainty-calibration/","title":"uncertainty-calibration","text":"Python library to measure the calibration error of models, including confidence intervals computed by Bootstrap resampling, and code to recalibrate models.
homepage: https://github.com/p-lambda/verified_calibration
version toolchain 0.0.9 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/unicore-uftp/","title":"unicore-uftp","text":"UNICORE Java-based client for UFTP
homepage: https://sourceforge.net/projects/unicore/
version versionsuffix toolchain 1.4.2 -Java-11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/unifdef/","title":"unifdef","text":"unifdef - selectively remove C preprocessor conditionals The unifdef utility selectively processes conditional C preprocessor and the additional text that they delimit, while otherwise leaving the file alone.
homepage: https://github.com/fanf2/unifdef
version toolchain 2.12 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/unimap/","title":"unimap","text":"Unimap is a fork of minimap2 optimized for assembly-to-reference alignment. It integrates the minigraph chaining algorithm and can align through long INDELs (up to 100kb by default) much faster than minimap2. Unimap is a better fit for resolving segmental duplications and is recommended over minimap2 for alignment between high-quality assemblies. Unimap does not replace minimap2 for other types of alignment. It drops the support of multi-part index and short-read mapping. Its long-read alignment is different from minimap2 but is not necessarily better. Unimap is more of a specialized minimap2 at the moment.
homepage: https://github.com/lh3/unimap
version toolchain 0.1 GCCcore/10.2.0 0.1 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/units/","title":"units","text":"GNU Units converts quantities expressed in various systems of measurement to their equivalents in other systems of measurement. Like many similar programs, it can handle multiplicative scale changes. It can also handle nonlinear conversions such as Fahrenheit to Celsius or wire gauge, and it can convert from and to sums of units, such as converting between meters and feet plus inches.
homepage: https://www.gnu.org/software/units/
version toolchain 2.19 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/unixODBC/","title":"unixODBC","text":"unixODBC provides a uniform interface between application and database driver
homepage: https://www.unixodbc.org
version toolchain 2.3.11 foss/2022b 2.3.12 GCCcore/12.3.0 2.3.7 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/unrar/","title":"unrar","text":"RAR is a powerful archive manager.
homepage: https://www.rarlab.com/
version toolchain 5.6.1 GCCcore/7.3.0 5.7.3 GCCcore/8.2.0 6.0.2 GCCcore/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/utf8proc/","title":"utf8proc","text":"utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding.
homepage: https://github.com/JuliaStrings/utf8proc
version toolchain 2.2.0 GCCcore/6.4.0 2.3.0 GCCcore/8.2.0 2.5.0 GCCcore/10.2.0 2.5.0 GCCcore/8.3.0 2.5.0 GCCcore/9.3.0 2.6.1 GCCcore/10.3.0 2.6.1 GCCcore/11.2.0 2.7.0 GCCcore/11.3.0 2.8.0 GCCcore/12.2.0 2.8.0 GCCcore/12.3.0 2.9.0 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/u/util-linux/","title":"util-linux","text":"Set of Linux utilities
homepage: http://www.kernel.org/pub/linux/utils/util-linux
version toolchain 2.27.1 foss/2016a 2.27.1 intel/2016a 2.28 foss/2016a 2.28 intel/2016a 2.28.1 intel/2016b 2.29 foss/2016b 2.29 intel/2016b 2.29.2 GCCcore/6.3.0 2.29.2 intel/2017a 2.30 GCCcore/6.4.0 2.30.1 GCCcore/6.3.0 2.30.1 foss/2017a 2.31 GCCcore/6.4.0 2.31.1 GCCcore/6.4.0 2.32 GCCcore/6.4.0 2.32 GCCcore/7.3.0 2.32.1 GCCcore/7.3.0 2.33 GCCcore/8.2.0 2.34 GCCcore/8.3.0 2.35 GCCcore/9.3.0 2.36 GCCcore/10.2.0 2.36 GCCcore/10.3.0 2.37 GCCcore/11.2.0 2.38 GCCcore/11.3.0 2.38.1 GCCcore/12.2.0 2.39 GCCcore/12.3.0 2.39 GCCcore/13.2.0 2.40 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/","title":"List of supported software (v)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- V8
- vaeda
- Vala
- Valgrind
- Vamb
- Vampir
- Vampire
- VAMPIRE-ASM
- VarDict
- variant_tools
- VariantMetaCaller
- VarScan
- vartools
- VASP
- VAtools
- vawk
- VBZ-Compression
- VCF-kit
- vcflib
- vcfnp
- VCFtools
- vConTACT2
- VEGAS
- velocyto
- Velvet
- VEP
- verifyBamID
- VERSE
- versioningit
- VESTA
- ViennaRNA
- vigra
- Vim
- VirSorter
- VirSorter2
- virtualenv
- VirtualGL
- Virtuoso-opensource
- visdom
- Visit
- vispr
- VisPy
- vitessce-python
- vitessceR
- VMD
- VMTK
- voltools
- vorbis-tools
- Voro++
- vsc-base
- vsc-install
- vsc-mympirun
- vsc-mympirun-scoop
- vsc-processcontrol
- VSCode
- VSEARCH
- vt
- VTK
- VTune
- VV
- VXL
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/V8/","title":"V8","text":"R interface to Google's open source JavaScript engine
homepage: https://cran.r-project.org/web/packages/V8/
version versionsuffix toolchain 2.2 -R-3.5.1 foss/2018b 2.3 -R-3.6.0 foss/2019a 2.3 -R-3.6.0 intel/2019a 3.2.0 -R-3.6.2 foss/2019b 3.4.0 -R-4.0.0 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VAMPIRE-ASM/","title":"VAMPIRE-ASM","text":"Vampire is designed from the ground-up to be an easy to use, fast, open-source and extensible software package capable of modelling almost any magnetic material with atomic resolution.
homepage: https://vampire.york.ac.uk/
version toolchain 6.0 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VASP/","title":"VASP","text":"The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.
homepage: http://www.vasp.at
version toolchain 5.4.1 intel/2016.02-GCC-4.9 6.3.2 nvofbf/2022.07 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VAtools/","title":"VAtools","text":"VAtools is a python package that includes several tools to annotate VCF files with data from other tools.
homepage: https://vatools.readthedocs.io/en/latest/
version versionsuffix toolchain 3.0.1 -Python-3.6.6 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VBZ-Compression/","title":"VBZ-Compression","text":"VBZ compression HDF5 plugin for nanopolish
homepage: https://github.com/nanoporetech/vbz_compression
version toolchain 1.0.1 gompi/2020b 1.0.3 gompi/2022a 1.0.3 gompi/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VCF-kit/","title":"VCF-kit","text":"VCF-kit is a command-line based collection of utilities for performing analysis on Variant Call Format (VCF) files.
homepage: https://github.com/AndersenLab/VCF-kit
version versionsuffix toolchain 0.1.6 -Python-2.7.15 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VCFtools/","title":"VCFtools","text":"The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
homepage: https://vcftools.github.io
version versionsuffix toolchain 0.1.14 -Perl-5.22.1 foss/2016a 0.1.14 -Perl-5.22.1 intel/2016a 0.1.15 -Perl-5.24.0 foss/2016b 0.1.15 -Perl-5.26.0 foss/2017b 0.1.15 -Perl-5.26.1 foss/2018a 0.1.15 -Perl-5.26.0 intel/2017b 0.1.16 GCC/10.2.0 0.1.16 GCC/10.3.0 0.1.16 GCC/11.2.0 0.1.16 GCC/11.3.0 0.1.16 GCC/12.2.0 0.1.16 GCC/12.3.0 0.1.16 GCC/8.3.0 0.1.16 GCC/9.3.0 0.1.16 -Perl-5.28.0 foss/2018b 0.1.16 iccifort/2019.5.281 0.1.16 -Perl-5.28.0 intel/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VEGAS/","title":"VEGAS","text":"VEGAS (Versatile Gene-based Association Study) is a free program for performing gene-based tests for association using the results from genetic association studies
homepage: http://gump.qimr.edu.au/VEGAS/
version toolchain 0.8.27 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VEP/","title":"VEP","text":"Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP.
homepage: https://www.ensembl.org/info/docs/tools/vep
version versionsuffix toolchain 103.1 GCC/10.2.0 105 GCC/11.2.0 107 GCC/11.3.0 111 GCC/12.2.0 93.4 -Perl-5.26.1 intel/2018a 94.0 -Perl-5.28.0 foss/2018b 94.5 -Perl-5.26.0 foss/2017b 94.5 -Perl-5.26.0 intel/2017b 95.0 -Perl-5.28.0 foss/2018b 96.0 -Perl-5.28.1 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VERSE/","title":"VERSE","text":"A versatile and efficient RNA-Seq read counting tool
homepage: https://github.com/qinzhu/VERSE
version toolchain 0.1.5 foss/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VESTA/","title":"VESTA","text":"VESTA is a 3D visualization program for structured models, volumetric data such as electron/nuclear densities, and crystal morphologies.
homepage: http://www.jp-minerals.org/vesta
version versionsuffix toolchain 3.5.8 -gtk3 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VMD/","title":"VMD","text":"VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
homepage: http://www.ks.uiuc.edu/Research/vmd
version versionsuffix toolchain 1.9.3 -Python-2.7.14 foss/2017b 1.9.3 -Python-2.7.12 intel/2016b 1.9.3 -Python-2.7.14 intel/2018a 1.9.3 -Python-2.7.15 intel/2018b 1.9.4a43 -Python-3.7.4 fosscuda/2019b 1.9.4a51 foss/2020b 1.9.4a51 fosscuda/2020b 1.9.4a57 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VMTK/","title":"VMTK","text":"vmtk is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.
homepage: https://vmtk.org
version versionsuffix toolchain 1.4.0 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VSCode/","title":"VSCode","text":"Visual Studio Code is a lightweight but powerful source code editor which runs on your desktop and is available for Windows, macOS and Linux. It comes with built-in support for JavaScript, TypeScript and Node.js and has a rich ecosystem of extensions for other languages and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin your journey with VS Code with these introductory videos.
homepage: https://code.visualstudio.com/
version toolchain 1.85.0 system 1.88.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VSEARCH/","title":"VSEARCH","text":"VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.
homepage: https://github.com/torognes/vsearch
version toolchain 2.13.4 iccifort/2019.1.144-GCC-8.2.0-2.31.1 2.15.0 GCC/9.3.0 2.18.0 GCC/10.2.0 2.21.1 GCC/10.3.0 2.22.1 GCC/11.3.0 2.25.0 GCC/12.3.0 2.28.1 GCC/10.2.0 2.9.1 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VTK/","title":"VTK","text":"The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.
homepage: http://www.vtk.org
version versionsuffix toolchain 6.3.0 -Python-2.7.11 foss/2016a 6.3.0 -Python-2.7.12 foss/2016b 6.3.0 -Python-2.7.11 intel/2016a 6.3.0 -Python-2.7.12 intel/2016b 7.0.0 -Python-2.7.12 intel/2016b 7.1.0 -Python-2.7.12 intel/2016b 7.1.1 -Python-2.7.13 intel/2017a 8.0.1 -Python-2.7.14 foss/2017b 8.0.1 -Python-2.7.14 intel/2017b 8.1.0 -Python-2.7.14 foss/2018a 8.1.0 -Python-3.6.4 foss/2018a 8.1.0 -Python-2.7.14 intel/2018a 8.1.0 -Python-3.6.4 intel/2018a 8.1.1 -Python-2.7.15 foss/2018b 8.1.1 -Python-3.6.6 foss/2018b 8.1.1 -Python-3.6.6 fosscuda/2018b 8.1.1 -Python-2.7.14 intel/2018a 8.2.0 -Python-2.7.15 foss/2019a 8.2.0 -Python-3.7.2 foss/2019a 8.2.0 -Python-2.7.16 foss/2019b 8.2.0 -Python-3.7.4 foss/2019b 8.2.0 -Python-3.8.2 foss/2020a 8.2.0 foss/2021a 8.2.0 -Python-3.8.2 fosscuda/2020a 8.2.0 -Python-3.7.2 intel/2019a 8.2.0 -Python-3.8.2 intel/2020a 9.0.1 foss/2020b 9.0.1 foss/2021a 9.0.1 fosscuda/2020b 9.1.0 foss/2021b 9.2.0.rc2 foss/2022a 9.2.2 foss/2022a 9.2.6 foss/2022b 9.2.6 foss/2023a 9.3.0 foss/2023a 9.3.0 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VTune/","title":"VTune","text":"Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.
homepage: http://software.intel.com/en-us/intel-vtune-amplifier-xe
version toolchain 2013_update10 system 2013_update11 system 2013_update12 system 2013_update6 system 2013_update8 system 2013_update9 system 2016_update3 system 2017 system 2017_update1 system 2017_update2 system 2017_update3 system 2018_update1 system 2018_update2 system 2018_update3 system 2019_update2 system 2019_update3 system 2019_update5 system 2020_update3 system 2021.6.0 system 2021.9.0 system 2022.0.0 system 2022.2.0 system 2022.3.0 system 2023.2.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VV/","title":"VV","text":"VV is an open-source and cross platform image viewer, designed for fast and simple visualization of spatio-temporal images: 2D, 2D+t, 3D and 3D+t (or 4D) images. Only the command-line (clitk) tools are build.
homepage: https://www.creatis.insa-lyon.fr/rio/vv
version versionsuffix toolchain 2018.09.19 -Python-3.6.6 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VXL/","title":"VXL","text":"A multi-platform collection of C++ software libraries for Computer Vision and Image Understanding.
homepage: https://sf.net/projects/vxl
version toolchain 1.18.0 foss/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/Vala/","title":"Vala","text":"Vala is a programming language using modern high level abstractions without imposing additional runtime requirements and without using a different ABI compared to applications and libraries written in C.
homepage: https://wiki.gnome.org/Projects/Vala
version toolchain 0.52.4 GCCcore/10.3.0 0.56.14 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/Valgrind/","title":"Valgrind","text":"Valgrind: Debugging and profiling tools
homepage: http://valgrind.org/downloads/
version toolchain 3.11.0 foss/2016a 3.11.0 intel/2016a 3.13.0 foss/2017b 3.13.0 foss/2018a 3.13.0 intel/2017a 3.13.0 intel/2017b 3.13.0 intel/2018a 3.14.0 foss/2018b 3.16.1 gompi/2019b 3.16.1 gompi/2020a 3.16.1 gompi/2020b 3.16.1 iimpi/2020a 3.17.0 gompi/2021a 3.18.1 gompi/2021b 3.18.1 iimpi/2021b 3.19.0 gompi/2022a 3.20.0 gompi/2022a 3.21.0 gompi/2022b 3.21.0 gompi/2023a 3.23.0 gompi/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/Vamb/","title":"Vamb","text":"Vamb is a metagenomic binner which feeds sequence composition information from a contig catalogue and co-abundance information from BAM files into a variational autoencoder and clusters the latent representation.
homepage: https://github.com/RasmussenLab/vamb
version versionsuffix toolchain 3.0.9 -CUDA-11.5.2 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/Vampir/","title":"Vampir","text":"The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.
homepage: http://www.vampir.eu
version versionsuffix toolchain 8.4.1 -demo system 8.4.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/Vampire/","title":"Vampire","text":"The Vampire Theorem Prover.
homepage: https://vprover.github.io/
version toolchain 4.5.1 GCCcore/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VarDict/","title":"VarDict","text":"VarDict is an ultra sensitive variant caller for both single and paired sample variant calling from BAM files.
homepage: https://github.com/AstraZeneca-NGS/VarDict
version versionsuffix toolchain 1.5.7 -Perl-5.28.0 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VarScan/","title":"VarScan","text":"Variant calling and somatic mutation/CNV detection for next-generation sequencing data
homepage: http://varscan.sourceforge.net/
version versionsuffix toolchain 2.3.6 -Java-1.7.0_80 system 2.4.1 -Java-1.7.0_80 system 2.4.4 -Java-1.8 system 2.4.4 -Java-11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VariantMetaCaller/","title":"VariantMetaCaller","text":"VariantMetaCaller automatically integrates variant calling pipelines into a better performing overall model that also predicts accurate variant probabilities.
homepage: http://bioinformatics.mit.bme.hu/VariantMetaCaller/
version toolchain 1.0 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/Velvet/","title":"Velvet","text":"Sequence assembler for very short reads
homepage: https://github.com/dzerbino/velvet/
version versionsuffix toolchain 1.2.10 -mt-kmer_191 GCC/11.2.0 1.2.10 -mt-kmer_191 GCC/8.3.0 1.2.10 -mt-kmer_191 foss/2018a 1.2.10 -mt-kmer_191 foss/2018b 1.2.10 -mt-kmer_191 foss/2023a 1.2.10 -mt-kmer_37 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/ViennaRNA/","title":"ViennaRNA","text":"The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
homepage: http://www.tbi.univie.ac.at/RNA/
version versionsuffix toolchain 2.2.3 intel/2016b 2.3.4 foss/2016b 2.3.5 intel/2017a 2.4.10 -Python-2.7.15 foss/2018b 2.4.10 -Python-2.7.15 intel/2018b 2.4.11 -Python-3.6.6 foss/2018b 2.4.14 -Python-3.6.6 foss/2018b 2.5.0 foss/2021b 2.5.1 foss/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/Vim/","title":"Vim","text":"Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor 'Vi', with a more complete feature set.
homepage: http://www.vim.org
version versionsuffix toolchain 8.0 -Python-2.7.11 foss/2016a 8.1.0483 -Python-2.7.15 foss/2018b 8.1.1209 -Python-3.7.2 GCCcore/8.2.0 9.0.0950 GCCcore/11.3.0 9.0.1434 GCCcore/12.2.0 9.1.0004 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VirSorter/","title":"VirSorter","text":"VirSorter: mining viral signal from microbial genomic data.
homepage: https://github.com/simroux/VirSorter
version versionsuffix toolchain 1.0.6 foss/2021b 20160601 -Perl-5.22.1 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VirSorter2/","title":"VirSorter2","text":"VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.
homepage: https://github.com/jiarong/VirSorter2
version toolchain 2.2.4 foss/2021b 2.2.4 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VirtualGL/","title":"VirtualGL","text":"VirtualGL is an open source toolkit that gives any Linux or Unix remote display software the ability to run OpenGL applications with full hardware acceleration.
homepage: https://virtualgl.org/
version toolchain 2.6.1 foss/2018b 2.6.2 GCCcore/9.3.0 3.0 GCC/11.2.0 3.1 GCC/12.3.0 3.1.1 GCC/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/Virtuoso-opensource/","title":"Virtuoso-opensource","text":"Virtuoso is a high-performance and scalable Multi-Model RDBMS, Data Integration Middleware, Linked Data Deployment, and HTTP Application Server Platform.
homepage: https://github.com/openlink/virtuoso-opensource
version toolchain 7.2.6.1 GCC/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/VisPy/","title":"VisPy","text":"VisPy is a high-performance interactive 2D/3D data visualization library leveraging the computational power of modern Graphics Processing Units (GPUs) through the OpenGL library to display very large datasets.
homepage: https://vispy.org
version toolchain 0.12.2 foss/2022a 0.12.2 gfbf/2023a 0.14.1 foss/2023a 0.6.6 foss/2020b 0.6.6 intel/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/Visit/","title":"Visit","text":"VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. From Unix, Windows or Mac workstations, users can interactively visualize and analyze data ranging in scale from small (<101 core) desktop-sized projects to large (>105 core) leadership-class computing facility simulation campaigns. Users can quickly generate visualizations, animate them through time, manipulate them with a variety of operators and mathematical expressions, and save the resulting images and animations for presentations. VisIt contains a rich set of visualization features to enable users to view a wide variety of data including scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured, adaptive and unstructured meshes. Owing to its customizeable plugin design, VisIt is capabable of visualizing data from over 120 different scientific data formats.
homepage: https://github.com/visit-dav/visit
version toolchain 3.4.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/Voro%2B%2B/","title":"Voro++","text":"Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles.
homepage: http://math.lbl.gov/voro++/
version toolchain 0.4.6 GCCcore/10.2.0 0.4.6 GCCcore/10.3.0 0.4.6 GCCcore/11.2.0 0.4.6 GCCcore/11.3.0 0.4.6 GCCcore/12.2.0 0.4.6 GCCcore/12.3.0 0.4.6 GCCcore/6.4.0 0.4.6 GCCcore/9.3.0 0.4.6 foss/2016a 0.4.6 foss/2019b 0.4.6 intel/2016a 0.4.6 intel/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vConTACT2/","title":"vConTACT2","text":"vConTACT2 is a tool to perform guilt-by-contig-association classification of viral genomic sequence data.
homepage: https://bitbucket.org/MAVERICLab/vcontact2
version toolchain 0.11.3 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vaeda/","title":"vaeda","text":"vaeda (variaitonal auto-encoder (vae) for doublet annotation (da)) is a Python package for doublet annotation in single cell RNA-sequencing.
homepage: https://github.com/kostkalab/vaeda
version toolchain 0.0.30 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/variant_tools/","title":"variant_tools","text":"Variant tools is a software tool for the manipulation, annotation, selection, simulation, and analysis of variants in the context of next-gen sequencing analysis. Unlike some other tools used for Next-Gen sequencing analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.
homepage: https://vatlab.github.io/vat-docs/
version versionsuffix toolchain 3.1.3 -Python-3.7.4 foss/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vartools/","title":"vartools","text":"Command line utility that provides tools for processing and analyzing astronomical time series data.
homepage: https://www.astro.princeton.edu/~jhartman/vartools.html
version toolchain 1.35 foss/2016b 1.35 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vawk/","title":"vawk","text":"An awk-like VCF parser
homepage: https://github.com/cc2qe/vawk
version versionsuffix toolchain 0.0.1 -Python-2.7.18 GCCcore/10.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vcflib/","title":"vcflib","text":"vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals.
homepage: https://github.com/vcflib/vcflib
version versionsuffix toolchain 1.0.2 GCC/10.2.0 1.0.2 GCC/10.3.0 1.0.2 -Python-3.8.2 GCC/9.3.0 1.0.3 -R-4.1.0 foss/2021a 1.0.3 -R-4.1.2 foss/2021b 1.0.9 -R-4.2.1 foss/2022a 1.0.9 -R-4.2.2 foss/2022b 1.0.9 -R-4.3.2 gfbf/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vcfnp/","title":"vcfnp","text":"Load data from a VCF (variant call format) file into numpy arrays, and (optionally) from there into an HDF5 file.
homepage: https://github.com/alimanfoo/vcfnp
version versionsuffix toolchain 2.3.0 -Python-2.7.11 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/velocyto/","title":"velocyto","text":"Velocyto is a library for the analysis of RNA velocity.
homepage: https://velocyto.org/velocyto.py/
version versionsuffix toolchain 0.17.17 foss/2021a 0.17.17 foss/2022a 0.17.17 foss/2023a 0.17.17 -Python-3.8.2 intel/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/verifyBamID/","title":"verifyBamID","text":"verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When external genotypes are not available, verifyBamID still robustly detects sample swaps.
homepage: http://csg.sph.umich.edu/kang/verifyBamID/index.html
version toolchain 1.1.3 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/versioningit/","title":"versioningit","text":"versioningit is yet another Python packaging plugin for automatically determining your package\u2019s version based on your version control repository\u2019s tags. Unlike others, it allows easy customization of the version format and even lets you easily override the separate functions used for version extraction & calculation.
homepage: https://github.com/jwodder/versioningit
version toolchain 3.1.2 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vigra/","title":"vigra","text":"Vision with Generic Algorithms is an image processing and analysis library that puts its main emphasis on customizable algorithms and data structures.
homepage: https://ukoethe.github.io/vigra/
version toolchain 1.11.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/virtualenv/","title":"virtualenv","text":"A tool for creating isolated virtual python environments.
homepage: https://github.com/pypa/virtualenv
version toolchain 20.23.1 GCCcore/12.3.0 20.24.6 GCCcore/13.2.0 20.26.2 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/visdom/","title":"visdom","text":"A flexible tool for creating, organizing, and sharing visualizations of live, rich data. Supports Torch and Numpy.
homepage: https://github.com/fossasia/visdom
version toolchain 0.2.4 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vispr/","title":"vispr","text":"VISPR - A visualization framework for CRISPR data.
homepage: https://pypi.org/project/vispr/
version toolchain 0.4.14 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vitessce-python/","title":"vitessce-python","text":"Python API and Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce.
homepage: https://github.com/vitessce/vitessce-python
version toolchain 20230222 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vitessceR/","title":"vitessceR","text":"Vitessce is a visual integration tool for exploration of spatial single-cell experiments.
homepage: https://github.com/vitessce/vitessceR
version versionsuffix toolchain 0.99.0-20230110 -R-4.2.1 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/voltools/","title":"voltools","text":"CUDA-accelerated numpy 3D affine transformations
homepage: https://github.com/the-lay/voltools
version toolchain 0.4.2 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vorbis-tools/","title":"vorbis-tools","text":"Command-line tools for creating and playing Ogg Vorbis files.
homepage: https://xiph.org/vorbis/
version toolchain 1.4.2 GCCcore/10.2.0 1.4.2 GCCcore/10.3.0 1.4.2 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vsc-base/","title":"vsc-base","text":"VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.
homepage: http://hpcugent.github.com/vsc-mympirun/
version versionsuffix toolchain 1.6.9 system 1.7.3 system 2.0.4 system 2.1.2 system 2.4.17 -Python-2.7.11 intel/2016a 2.4.2 system 2.5.1 -Python-2.7.11 intel/2016a 2.5.1 -Python-2.7.12 intel/2016b 2.5.1 system 2.5.8 system 2.8.0 system 2.8.1 system 2.8.3 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vsc-install/","title":"vsc-install","text":"vsc-install provides shared setuptools functions and classes for Python libraries developed by UGent's HPC group
homepage: https://pypi.python.org/pypi/vsc-install
version versionsuffix toolchain 0.10.11 -Python-2.7.11 intel/2016a 0.10.11 -Python-2.7.12 intel/2016b 0.10.25 system 0.10.26 system 0.10.6 -Python-2.7.11 intel/2016a 0.10.6 system 0.11.1 system 0.11.2 system 0.9.18 -Python-2.7.11 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vsc-mympirun-scoop/","title":"vsc-mympirun-scoop","text":"VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.
homepage: http://hpcugent.github.com/vsc-mympirun/
version versionsuffix toolchain 3.4.1 -Python-2.7.12 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vsc-mympirun/","title":"vsc-mympirun","text":"VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.
homepage: https://github.com/hpcugent/vsc-mympirun/
version versionsuffix toolchain 3.2.1 system 3.3.0 system 3.4.2 -Python-2.7.11-vsc-base-2.4.17 intel/2016a 3.4.2 -Python-2.7.11-vsc-base-2.5.1 intel/2016a 3.4.2 -vsc-base-2.4.2 system 3.4.2 system 3.4.3 -Python-2.7.12 intel/2016b 4.0.0 system 4.0.0b0 system 4.0.1 system 4.0.2 system 4.1.4 system 4.1.5 system 4.1.6 system 4.1.8 system 4.1.9 system 5.1.0 system 5.2.0 system 5.2.10 system 5.2.11 system 5.2.2 system 5.2.3 system 5.2.4 system 5.2.5 system 5.2.6 system 5.2.7 system 5.2.9 system 5.3.0 system 5.3.1 system 5.4.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vsc-processcontrol/","title":"vsc-processcontrol","text":"vsc-processcontrol is a module to abstract process control like scheduler settings and affinity from actual implementations like vsc.affinity and psutil.
homepage: http://hpcugent.github.com/vsc-processcontrol/
version versionsuffix toolchain 1.0 -vsc-base-2.1.2 system 1.0 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/v/vt/","title":"vt","text":"A tool set for short variant discovery in genetic sequence data.
homepage: https://genome.sph.umich.edu/wiki/Vt
version toolchain 0.57721 GCC/10.2.0 0.57721 GCC/10.3.0 0.57721 GCC/11.2.0 0.57721 GCC/9.3.0 0.57721 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/","title":"List of supported software (w)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- waLBerla
- wandb
- Wannier90
- WannierTools
- Wayland
- Waylandpp
- WCSLIB
- WCT
- wcwidth
- webin-cli
- WebKitGTK+
- weblogo
- WebSocket++
- WEKA
- WFA2
- wfdb
- WGDgc
- wget
- wgsim
- WHAM
- WhatsHap
- wheel
- WIEN2k
- WildMagic
- Winnowmap
- WisecondorX
- WISExome
- wkhtmltopdf
- worker
- wpebackend-fdo
- WPS
- wradlib
- wrapt
- WRF
- WRF-Fire
- wrf-python
- WSClean
- wtdbg2
- wxPropertyGrid
- wxPython
- wxWidgets
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WCSLIB/","title":"WCSLIB","text":"The FITS \"World Coordinate System\" (WCS) standard defines keywords and usage that provide for the description of astronomical coordinate systems in a FITS image header.
homepage: https://www.atnf.csiro.au/people/mcalabre/WCS/
version toolchain 7.11 GCC/11.2.0 7.11 GCC/11.3.0 7.11 GCC/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WCT/","title":"WCT","text":"NOAA's Weather and Climate Toolkit (WCT) is free, platform independent software distributed from NOAA's National Centers for Environmental Information (NCEI). The WCT allows the visualization and data export of weather and climate data, including Radar, Satellite and Model data. The WCT also provides access to weather/climate web services provided from NCEI and other organizations.
homepage: https://www.ncdc.noaa.gov/wct/index.php
version versionsuffix toolchain 4.6.0 -Java-11 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WEKA/","title":"WEKA","text":"Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.
homepage: http://www.cs.waikato.ac.nz/ml/weka/index.html
version versionsuffix toolchain 3.6.12 -Java-1.7.0_80 system 3.7.0 -Java-1.7.0_80 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WFA2/","title":"WFA2","text":"The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process.
homepage: https://github.com/smarco/WFA2-lib
version toolchain 2.3.3 GCCcore/11.3.0 2.3.4 GCCcore/12.2.0 2.3.4 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WGDgc/","title":"WGDgc","text":"Analysis of whole genome duplications (WGD) and triplications (WGT) using comparative gene count data
homepage: https://github.com/cecileane/WGDgc
version versionsuffix toolchain 1.3 -R-4.3.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WHAM/","title":"WHAM","text":"An implementation of WHAM: the Weighted Histogram Analysis Method
homepage: http://membrane.urmc.rochester.edu/?page_id=126
version versionsuffix toolchain 2.0.10.2 -kj_mol intel/2020a 2.0.10.2 intel/2020a 2.0.9.1 -kj_mol intel/2019a 2.0.9.1 intel/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WIEN2k/","title":"WIEN2k","text":"The program package WIEN2k allows to perform electronic structure calculations of solids using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. WIEN2k is an all-electron scheme including relativistic effects and has many features.
homepage: http://www.wien2k.at/
version toolchain 17.1 foss/2018a 17.1 gimkl/2017a 17.1 intel/2018a 18.1 foss/2018a 18.1 gimkl/2017a 18.1 intel/2018a 19.1 intel/2019a 19.2 intel/2020b 21.1 intel/2021a 21.1 intel/2021b 23.2 intel/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WISExome/","title":"WISExome","text":"A within-sample comparison approach to detect copy number variations in whole exome sequencing data
homepage: https://github.com/VUmcCGP/wisexome
version versionsuffix toolchain 20180517 -Python-2.7.14 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WPS/","title":"WPS","text":"WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.
homepage: http://www.wrf-model.org
version versionsuffix toolchain 3.8.0 -dmpar intel/2016a 3.9.1 -dmpar foss/2020b 4.0.1 -dmpar intel/2018b 4.0.2 -dmpar foss/2018b 4.1 -dmpar intel/2019b 4.2 -dmpar foss/2020b 4.3.1 -dmpar foss/2021a 4.4 -dmpar foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WRF-Fire/","title":"WRF-Fire","text":"WRF-Fire combines the Weather Research and Forecasting model (WRF) with a fire code implementing a surface fire behavior model, called SFIRE, based on semi-empirical formulas calculate the rate of spread of the fire line (the interface between burning and unignited fuel) based on fuel properties, wind velocities from WRF, and terrain slope. The fire spread is implemented by the level set method.
homepage: http://www.openwfm.org/wiki/WRF-SFIRE
version versionsuffix toolchain 20170221 -dmpar intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WRF/","title":"WRF","text":"The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.
homepage: http://www.wrf-model.org
version versionsuffix toolchain 3.8.0 -dmpar intel/2016a 3.8.0 -dmpar intel/2016b 3.9.1.1 -dmpar foss/2020a 3.9.1.1 -dmpar foss/2020b 3.9.1.1 -dmpar intel/2020a 3.9.1.1 -dmpar intel/2020b 4.0.1 -dmpar intel/2018b 4.0.2 -dmpar foss/2018b 4.1.3 -dmpar foss/2019b 4.1.3 -dmpar foss/2020a 4.1.3 -dm+sm intel/2019b 4.1.3 -dmpar intel/2019b 4.2.2 -dmpar foss/2020b 4.3 -dmpar foss/2021a 4.4 -dmpar foss/2022a 4.4.1 -dmpar foss/2022b 4.5.1 -dmpar foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WSClean/","title":"WSClean","text":"WSClean (w-stacking clean) is a fast generic widefield imager. It implements several gridding algorithms and offers fully-automated multi-scale multi-frequency deconvolution.
homepage: https://wsclean.readthedocs.io/
version toolchain 3.4 foss/2022a 3.4 foss/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/Wannier90/","title":"Wannier90","text":"A tool for obtaining maximally-localised Wannier functions
homepage: http://www.wannier.org
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","boost":0.5},{"location":"version-specific/supported-software/w/WannierTools/","title":"WannierTools","text":"an open-source software package for novel topological materials
homepage: http://www.wanniertools.com/
version toolchain 2.3.0 intel/2018a 2.5.1 intel/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/Wayland/","title":"Wayland","text":"Wayland is a project to define a protocol for a compositor to talk to its clients as well as a library implementation of the protocol. The compositor can be a standalone display server running on Linux kernel modesetting and evdev input devices, an X application, or a wayland client itself. The clients can be traditional applications, X servers (rootless or fullscreen) or other display servers.
homepage: https://wayland.freedesktop.org/
version toolchain 1.20.0 GCCcore/11.3.0 1.21.0 GCCcore/11.2.0 1.21.0 GCCcore/11.3.0 1.22.0 GCCcore/12.2.0 1.22.0 GCCcore/12.3.0 1.22.0 GCCcore/13.2.0 1.23.0 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/Waylandpp/","title":"Waylandpp","text":"Wayland is an object oriented display protocol, which features request and events. Requests can be seen as method calls on certain objects, whereas events can be seen as signals of an object. This makes the Wayland protocol a perfect candidate for a C++ binding. The goal of this library is to create such a C++ binding for Wayland using the most modern C++ technology currently available, providing an easy to use C++ API to Wayland.
homepage: https://github.com/NilsBrause/waylandpp
version toolchain 1.0.0 GCCcore/11.2.0 1.0.0 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WebKitGTK%2B/","title":"WebKitGTK+","text":"WebKitGTK+ is a full-featured port of the WebKit rendering engine, suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers. It offers WebKit\u2019s full functionality and is useful in a wide range of systems from desktop computers to embedded systems like phones, tablets, and televisions.
homepage: https://webkitgtk.org/
version toolchain 2.24.1 GCC/8.2.0-2.31.1 2.27.4 GCC/10.3.0 2.27.4 GCC/8.3.0 2.37.1 GCC/11.2.0 2.40.4 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WebSocket%2B%2B/","title":"WebSocket++","text":"WebSocket++ is an open source (BSD license) header only C++ library that implements RFC6455 The WebSocket Protocol.
homepage: https://www.zaphoyd.com/websocketpp/
version toolchain 0.8.1 gompi/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WhatsHap/","title":"WhatsHap","text":"WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.
homepage: https://whatshap.readthedocs.io
version toolchain 1.1 foss/2020b 1.1 foss/2021a 1.4 foss/2021b 1.7 foss/2022a 2.1 foss/2022b 2.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WildMagic/","title":"WildMagic","text":"Wild Magic 5.17
homepage: https://www.geometrictools.com/index.html
version toolchain 5.17 GCCcore/10.3.0 5.17 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/Winnowmap/","title":"Winnowmap","text":"Winnowmap is a long-read mapping algorithm, and a result of our exploration into superior minimizer sampling techniques.
homepage: https://github.com/marbl/Winnowmap
version toolchain 1.0 GCC/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/WisecondorX/","title":"WisecondorX","text":"WisecondorX -- an evolved WISECONDOR
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version versionsuffix toolchain 1.1.6 -Python-3.8.2 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/waLBerla/","title":"waLBerla","text":"Widely applicable Lattics-Boltzmann from Erlangen is a block-structured high-performance framework for multiphysics simulations
homepage: https://walberla.net/index.html
version toolchain 6.1 foss/2021a 6.1 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/wandb/","title":"wandb","text":"CLI and Python API for Weights and Biases: a tool for visualizing and tracking your machine learning experiments.
homepage: https://www.wandb.com/
version versionsuffix toolchain 0.13.4 GCCcore/11.3.0 0.13.6 GCC/11.3.0 0.16.1 GCC/12.3.0 0.8.30 -Python-3.7.4 gcccuda/2019b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/wcwidth/","title":"wcwidth","text":"wcwidth is a low-level Python library to simplify Terminal emulation.
homepage: https://github.com/jquast/wcwidth
version versionsuffix toolchain 0.1.7 -Python-2.7.11 foss/2016a 0.1.7 -Python-3.5.1 foss/2016a 0.1.7 -Python-2.7.12 foss/2016b 0.1.7 -Python-2.7.12 intel/2016b 0.1.7 -Python-3.5.2 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/webin-cli/","title":"webin-cli","text":"The Webin command line submission interface can be used to validate, upload and submit files to the European Nucleotide Archive (ENA)
homepage: https://github.com/enasequence/webin-cli
version toolchain 1.8.9 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/weblogo/","title":"weblogo","text":"WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.
homepage: https://weblogo.berkeley.edu
version toolchain 2.8.2 foss/2022b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/wfdb/","title":"wfdb","text":"The native Python waveform-database (WFDB) package. A library of tools for reading, writing, and processing WFDB signals and annotations.
homepage: https://wfdb.readthedocs.io/en/latest/
version toolchain 4.1.2 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/wget/","title":"wget","text":"GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.
homepage: https://www.gnu.org/software/wget/
version toolchain 1.17.1 foss/2016a 1.17.1 foss/2016b 1.19.4 GCCcore/6.4.0 1.20.1 GCCcore/7.3.0 1.20.1 GCCcore/8.3.0 1.20.3 GCCcore/10.2.0 1.20.3 GCCcore/9.3.0 1.21.1 GCCcore/10.3.0 1.21.2 GCCcore/11.2.0 1.21.3 GCCcore/11.3.0 1.21.4 GCCcore/12.2.0 1.21.4 GCCcore/13.2.0 1.24.5 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/wgsim/","title":"wgsim","text":"Wgsim is a small tool for simulating sequence reads from a reference genome.
homepage: https://github.com/lh3/wgsim/
version toolchain 20111017 GCC/10.2.0 20111017 GCC/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/wheel/","title":"wheel","text":"A built-package format for Python.
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version versionsuffix toolchain 0.29.0 -Python-2.7.11 foss/2016a 0.29.0 -Python-3.5.1 foss/2016a 0.30.0 -Python-2.7.14 foss/2017b 0.30.0 -Python-3.6.3 foss/2017b 0.30.0 -Python-3.6.4 foss/2018a 0.30.0 -Python-2.7.14 fosscuda/2017b 0.30.0 -Python-3.6.3 fosscuda/2017b 0.30.0 -Python-2.7.14 intel/2017b 0.30.0 -Python-3.6.3 intel/2017b 0.30.0 -Python-3.6.4 intel/2018a 0.30.0 -Python-2.7.14 intelcuda/2017b 0.30.0 -Python-3.6.3 intelcuda/2017b 0.31.0 -Python-3.6.4 foss/2018a 0.31.0 -Python-2.7.14 fosscuda/2018a 0.31.0 -Python-3.6.4 fosscuda/2018a 0.31.0 -Python-2.7.14 intel/2018a 0.31.1 -Python-3.6.6 foss/2018b 0.31.1 -Python-2.7.15 fosscuda/2018b 0.31.1 -Python-3.6.6 fosscuda/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/wkhtmltopdf/","title":"wkhtmltopdf","text":"wkhtmltopdf and wkhtmltoimage are open source (LGPLv3) command line tools to render HTML into PDF and various image formats using the Qt WebKit rendering engine. These run entirely headless and do not require a display or display service.
homepage: http://wkhtmltopdf.org/
version versionsuffix toolchain 0.12.3 -Linux-x86_64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/worker/","title":"worker","text":"The Worker framework has been developed to help deal with parameter exploration experiments that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.
homepage: https://github.com/gjbex/worker
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","boost":0.5},{"location":"version-specific/supported-software/w/wpebackend-fdo/","title":"wpebackend-fdo","text":"WPE WebKit allows embedders to create simple and performant systems based on Web platform technologies. It is a WebKit port designed with flexibility and hardware acceleration in mind, leveraging common 3D graphics APIs for best performance.
homepage: https://wpewebkit.org/
version toolchain 1.13.1 GCCcore/11.2.0 1.14.1 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/wradlib/","title":"wradlib","text":"The wradlib project has been initiated in order to facilitate the use of weather radar data as well as to provide a common platform for research on new algorithms.
homepage: https://docs.wradlib.org/
version toolchain 2.0.3 foss/2022a 2.0.3 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://pypi.org/project/wrapt/
version toolchain 1.15.0 foss/2022a 1.15.0 gfbf/2022b 1.15.0 gfbf/2023a 1.15.0 intel/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/w/wrf-python/","title":"wrf-python","text":"A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model.
homepage: https://wrf-python.readthedocs.io
version versionsuffix toolchain 1.2.0 -Python-3.6.4 intel/2018a 1.3.1 -Python-3.6.6 intel/2018b 1.3.4.1 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://github.com/ruanjue/wtdbg2
version toolchain 2.3 GCC/7.3.0-2.30 2.5 GCCcore/11.2.0 2.5 GCCcore/11.3.0 2.5 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: http://wxpropgrid.sourceforge.net/
version toolchain 1.4.15 GCC/4.9.2 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://www.wxwidgets.org
version toolchain 3.0.3 foss/2018a 3.0.4 GCC/8.2.0-2.31.1 3.1.3 GCC/8.3.0 3.1.4 GCC/10.2.0 3.1.5 GCC/10.3.0 3.1.5 GCC/11.2.0 3.2.0 GCC/11.2.0 3.2.1 GCC/11.3.0 3.2.2.1 GCC/12.2.0 3.2.2.1 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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- Xerces-C++
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- xmlf90
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(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/X11/","title":"X11","text":"The X Window System (X11) is a windowing system for bitmap displays
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version toolchain 20160819 GCCcore/5.4.0 20160819 foss/2016b 20160819 intel/2016b 20170129 GCCcore/6.3.0 20170129 gimkl/2017a 20170314 GCCcore/6.3.0 20171023 GCCcore/6.4.0 20180131 GCCcore/6.4.0 20180604 GCCcore/7.3.0 20190311 GCCcore/8.2.0 20190717 GCCcore/8.3.0 20200222 GCCcore/9.3.0 20201008 GCCcore/10.2.0 20210518 GCCcore/10.3.0 20210802 GCCcore/11.2.0 20220504 GCCcore/11.3.0 20221110 GCCcore/12.2.0 20230603 GCCcore/12.3.0 20231019 GCCcore/13.2.0 20240607 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/XALT/","title":"XALT","text":"XALT 2 is a tool to allow a site to track user executables and library usage on a cluster. When installed it can tell a site what are the top executables by Node-Hours or by the number of users or the number of times it is run. XALT 2 also tracks library usage as well. XALT 2 can also track package use by R, MATLAB or Python. It tracks both MPI and non-MPI programs.
homepage: https://github.com/xalt/xalt
version toolchain 2.8.4 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/XBeach/","title":"XBeach","text":"XBeach is a two-dimensional model for wave propagation, long waves and mean flow, sediment transport and morphological changes of the nearshore area, beaches, dunes and backbarrier during storms.
homepage: https://oss.deltares.nl/web/xbeach
version toolchain 20230831 gompi/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/XCFun/","title":"XCFun","text":"Arbitrary order exchange-correlation functional library
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version versionsuffix toolchain 2.1.0 GCCcore/9.3.0 2.1.1 GCCcore/10.2.0 2.1.1 GCCcore/10.3.0 2.1.1 GCCcore/11.3.0 2.1.1 GCCcore/12.2.0 20180122 -Python-2.7.14 intel/2017b 20190127 -Python-3.7.2 foss/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/XCrySDen/","title":"XCrySDen","text":"XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
homepage: http://www.xcrysden.org/
version toolchain 1.5.60 intel/2019a 1.6.2 foss/2019b 1.6.2 foss/2020b 1.6.2 foss/2022a 1.6.2 intel/2019b 1.6.2 intel/2021b 1.6.2 intel/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: https://github.com/dmlc/xgboost
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","boost":0.5},{"location":"version-specific/supported-software/x/XGrafix/","title":"XGrafix","text":"A graphics library and controller for physics simulation programs. 3-d surface plots, scatter plots, 2-d line plots.
homepage: https://ptsg.egr.msu.edu/
version toolchain 2.41 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/XKeyboardConfig/","title":"XKeyboardConfig","text":"The non-arch keyboard configuration database for X Window. The goal is to provide the consistent, well-structured, frequently released open source of X keyboard configuration data for X Window System implementations (free, open source and commercial). The project is targeted to XKB-based systems.
homepage: http://www.freedesktop.org/wiki/Software/XKeyboardConfig/
version toolchain 2.17 foss/2016a 2.17 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/XMDS2/","title":"XMDS2","text":"The purpose of XMDS2 is to simplify the process of creating simulations that solve systems of initial-value first-order partial and ordinary differential equations.
homepage: http://www.xmds.org/
version versionsuffix toolchain 2.2.3 -Python-2.7.15 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/XML-Compile/","title":"XML-Compile","text":"Perl module for compilation based XML processing
homepage: https://metacpan.org/pod/XML::Compile
version toolchain 1.63 GCCcore/11.2.0 1.63 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/XML-LibXML/","title":"XML-LibXML","text":"Perl binding for libxml2
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","boost":0.5},{"location":"version-specific/supported-software/x/XML-Parser/","title":"XML-Parser","text":"This is a Perl extension interface to James Clark's XML parser, expat.
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","boost":0.5},{"location":"version-specific/supported-software/x/XMLSec/","title":"XMLSec","text":"XML Security Library is a C library based on LibXML2, supporting major XML security standards.
homepage: https://www.aleksey.com/xmlsec/index.html
version toolchain 1.2.26 GCCcore/6.4.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: http://xmlstar.sourceforge.net
version toolchain 1.6.1 GCCcore/6.4.0 1.6.1 foss/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/XOOPIC/","title":"XOOPIC","text":"XOOPIC is a two-dimensional 3-velocity particle-in-cell simulator. It can handle electrostatic and electromagnetic models, has a large variety of boundary conditions, supports multiple gasses and gas chemistry, and is easily reconfigurable via an input file.
homepage: https://github.com/rinku-mishra/xoopic
version toolchain 20210302 foss/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/XPLOR-NIH/","title":"XPLOR-NIH","text":"A System for X-ray Crystallography and NMR
homepage: https://nmr.cit.nih.gov/xplor-nih/
version versionsuffix toolchain 3.4 -Linux_x86_64 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/XSD/","title":"XSD","text":"CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to C++ data binding compiler.
homepage: https://www.codesynthesis.com/products/xsd/
version toolchain 4.0.0 GCCcore/8.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/XTandem/","title":"XTandem","text":"X!Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification.
homepage: https://www.thegpm.org/tandem
version toolchain 17.02.01.4 GCC/6.4.0-2.28 17.02.01.4 iccifort/2017.4.196-GCC-6.4.0-2.28 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
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homepage: http://tukaani.org/xz/
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","boost":0.5},{"location":"version-specific/supported-software/x/Xerces-C%2B%2B/","title":"Xerces-C++","text":"Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.
homepage: http://xerces.apache.org/xerces-c/
version toolchain 3.1.4 GCCcore/6.4.0 3.2.0 GCCcore/7.3.0 3.2.2 GCCcore/8.2.0 3.2.2 GCCcore/8.3.0 3.2.3 GCCcore/10.2.0 3.2.3 GCCcore/10.3.0 3.2.3 GCCcore/11.2.0 3.2.3 GCCcore/9.3.0 3.2.4 GCCcore/11.3.0 3.2.4 GCCcore/12.2.0 3.2.4 GCCcore/12.3.0 3.2.5 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/XlsxWriter/","title":"XlsxWriter","text":"A Python module for creating Excel XLSX files
homepage: https://xlsxwriter.readthedocs.io/
version toolchain 1.4.0 GCCcore/10.2.0 1.4.4 GCCcore/10.3.0 3.0.2 GCCcore/11.2.0 3.0.8 GCCcore/11.3.0 3.1.2 GCCcore/12.2.0 3.1.3 GCCcore/12.3.0 3.1.9 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/Xmipp/","title":"Xmipp","text":"Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.
homepage: https://github.com/I2PC/scipion/wiki
version versionsuffix toolchain 3.19.04-Apollo -Python-2.7.15 foss/2019a 3.19.04-Apollo -Python-2.7.15 fosscuda/2019a 3.22.07-Helios -CUDA-11.7.0 foss/2022a 3.22.07-Helios foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/Xvfb/","title":"Xvfb","text":"Xvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory.
homepage: https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml
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","boost":0.5},{"location":"version-specific/supported-software/x/x13as/","title":"x13as","text":"X-13ARIMA-SEATS is seasonal adjustment software produced, distributed, and maintained by the Census Bureau. Features of X-13ARIMA-SEATS include: - Extensive time series modeling and model selection capabilities for linear regression models with ARIMA errors (regARIMA models); - The capability to generate ARIMA model-based seasonal adjustment using a version of the SEATS software originally developed by Victor G\u00f3mez and Agust\u00edn Maravall at the Bank of Spain, as well as nonparametric adjustments from the X-11 procedure; - Diagnostics of the quality and stability of the adjustments achieved under the options selected; - The ability to efficiently process many series at once.
homepage: https://www.census.gov/data/software/x13as.About_X-13.html
version toolchain 1-1-b59 GCCcore/10.2.0 1-1-b59 GCCcore/11.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/x264/","title":"x264","text":"x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.
homepage: http://www.videolan.org/developers/x264.html
version toolchain 20160114 gimkl/2.11.5 20160114 intel/2016a 20160430 foss/2016a 20160430 intel/2016a 20160614 foss/2016b 20160614 intel/2016b 20170406 gimkl/2017a 20170721 GCCcore/6.4.0 20170913 intel/2017a 20171217 foss/2017b 20171217 intel/2017b 20180128 GCCcore/6.4.0 20180325 GCCcore/6.4.0 20181203 GCCcore/7.3.0 20190413 GCCcore/8.2.0 20190925 GCCcore/8.3.0 20191217 GCCcore/9.3.0 20201026 GCCcore/10.2.0 20210414 GCCcore/10.3.0 20210613 GCCcore/11.2.0 20220620 GCCcore/11.3.0 20230226 GCCcore/12.2.0 20230226 GCCcore/12.3.0 20231019 GCCcore/13.2.0 20240513 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/x265/","title":"x265","text":"x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL.
homepage: http://x265.org/
version toolchain 2.4 foss/2016b 2.5 intel/2017a 2.6 GCCcore/6.4.0 2.6 intel/2017b 2.7 GCCcore/6.4.0 2.9 GCCcore/7.3.0 3.0 GCCcore/8.2.0 3.2 GCCcore/8.3.0 3.3 GCCcore/10.2.0 3.3 GCCcore/9.3.0 3.5 GCCcore/10.3.0 3.5 GCCcore/11.2.0 3.5 GCCcore/11.3.0 3.5 GCCcore/12.2.0 3.5 GCCcore/12.3.0 3.5 GCCcore/13.2.0 3.6 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xCell/","title":"xCell","text":"xCell is a gene signatures-based method learned from thousands of pure cell types from various sources.
homepage: https://github.com/dviraran/xCell
version versionsuffix toolchain 1.12 -R-3.5.1 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xESMF/","title":"xESMF","text":"xESMF: Universal Regridder for Geospatial Data
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version versionsuffix toolchain 0.3.0 -Python-3.8.2 foss/2020a 0.3.0 intel/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xarray/","title":"xarray","text":"xarray (formerly xray) is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures.
homepage: https://github.com/pydata/xarray
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","boost":0.5},{"location":"version-specific/supported-software/x/xbitmaps/","title":"xbitmaps","text":"provides bitmaps for x
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","boost":0.5},{"location":"version-specific/supported-software/x/xcb-proto/","title":"xcb-proto","text":"The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
homepage: http://xcb.freedesktop.org/
version toolchain 1.11 system 1.13 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xcb-util-image/","title":"xcb-util-image","text":"The xcb-util-image package provides additional extensions to the XCB library.
homepage: http://xcb.freedesktop.org/
version toolchain 0.4.0 foss/2016a 0.4.0 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xcb-util-keysyms/","title":"xcb-util-keysyms","text":"The xcb-util-keysyms package contains a library for handling standard X key constants and conversion to/from keycodes.
homepage: http://xcb.freedesktop.org/
version toolchain 0.4.0 foss/2016a 0.4.0 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xcb-util-renderutil/","title":"xcb-util-renderutil","text":"The xcb-util-renderutil package provides additional extensions to the XCB library.
homepage: http://xcb.freedesktop.org/
version toolchain 0.3.9 foss/2016a 0.3.9 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xcb-util-wm/","title":"xcb-util-wm","text":"The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM.
homepage: http://xcb.freedesktop.org/
version toolchain 0.4.1 foss/2016a 0.4.1 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xcb-util/","title":"xcb-util","text":"The xcb-util package provides additional extensions to the XCB library, many that were previously found in Xlib, but are not part of core X protocol
homepage: http://xcb.freedesktop.org/
version toolchain 0.4.0 foss/2016a 0.4.0 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xclip/","title":"xclip","text":"xclip is a command line utility that is designed to run on any system with an X11 implementation.
homepage: https://github.com/astrand/xclip
version toolchain 0.13 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xdotool/","title":"xdotool","text":"xdotool lets you simulate keyboard input and mouse activity, move and resize windows, etc. It does this using X11\u2019s XTEST extension and other Xlib functions.
homepage: https://github.com/jordansissel/xdotool
version toolchain 3.20211022.1 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xextproto/","title":"xextproto","text":"XExtProto protocol headers.
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 7.3.0 foss/2016a 7.3.0 gimkl/2.11.5 7.3.0 intel/2016a 7.3.0 intel/2017b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xf86vidmodeproto/","title":"xf86vidmodeproto","text":"X11 XFree86 video mode extension protocol headers.
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 2.3.1 foss/2016a 2.3.1 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xineramaproto/","title":"xineramaproto","text":"X protocol and ancillary headers for xinerama
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.2.1 foss/2016a 1.2.1 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xmitgcm/","title":"xmitgcm","text":"xmitgcm is a python package for reading MITgcm binary MDS files into xarray data structures. By storing data in dask arrays, xmitgcm enables parallel, out-of-core analysis of MITgcm output data.
homepage: https://github.com/MITgcm/xmitgcm
version toolchain 0.5.2 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xmlf90/","title":"xmlf90","text":"xmlf90 is a basic XML parsing library written in Fortran.
homepage: https://launchpad.net/xmlf90
version toolchain 1.5.3 foss/2016b 1.5.3 foss/2017a 1.5.4 GCC/10.2.0 1.5.4 GCC/10.3.0 1.5.4 GCC/11.2.0 1.5.4 iccifort/2019.5.281 1.5.4 iccifort/2020.4.304 1.5.4 intel-compilers/2021.2.0 1.5.4 intel-compilers/2021.4.0 1.5.6 GCC/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xonsh/","title":"xonsh","text":"Xonsh is a Python-ish, BASHwards-looking shell language and command prompt.
homepage: https://xon.sh/
version toolchain 0.3.2 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xorg-macros/","title":"xorg-macros","text":"X.org macros utilities.
homepage: https://cgit.freedesktop.org/xorg/util/macros
version toolchain 1.19.0 foss/2016a 1.19.0 foss/2016b 1.19.0 gimkl/2.11.5 1.19.0 intel/2016a 1.19.0 intel/2016b 1.19.1 GCCcore/6.3.0 1.19.1 GCCcore/6.4.0 1.19.2 GCCcore/10.2.0 1.19.2 GCCcore/7.2.0 1.19.2 GCCcore/7.3.0 1.19.2 GCCcore/8.2.0 1.19.2 GCCcore/8.3.0 1.19.2 GCCcore/9.2.0 1.19.2 GCCcore/9.3.0 1.19.3 GCCcore/10.3.0 1.19.3 GCCcore/11.2.0 1.19.3 GCCcore/11.3.0 1.19.3 GCCcore/12.2.0 1.20.0 GCCcore/12.3.0 1.20.0 GCCcore/13.2.0 1.20.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xpdf/","title":"xpdf","text":"Xpdf was first released in 1995. It was written, and is still developed, by Derek Noonburg. Xpdf is a free PDF viewer and toolkit, including a text extractor, image converter, HTML converter, and more. Most of the tools are available as open source.
homepage: https://www.xpdfreader.com/
version toolchain 4.04 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xprop/","title":"xprop","text":"The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information.
homepage: http://www.x.org/wiki/
version versionsuffix toolchain 1.2.2 GCCcore/5.4.0 1.2.2 -X11-20180131 GCCcore/6.4.0 1.2.2 GCCcore/6.4.0 1.2.2 foss/2016a 1.2.2 foss/2016b 1.2.2 intel/2016a 1.2.2 intel/2016b 1.2.2 intel/2017a 1.2.3 GCCcore/7.3.0 1.2.4 GCCcore/8.2.0 1.2.4 GCCcore/8.3.0 1.2.4 GCCcore/9.3.0 1.2.5 GCCcore/10.2.0 1.2.5 GCCcore/10.3.0 1.2.5 GCCcore/11.2.0 1.2.5 GCCcore/11.3.0 1.2.5 GCCcore/12.2.0 1.2.6 GCCcore/12.3.0 1.2.7 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xproto/","title":"xproto","text":"X protocol and ancillary headers
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 7.0.28 foss/2016a 7.0.28 gimkl/2.11.5 7.0.28 intel/2016a 7.0.29 intel/2016a 7.0.31 GCCcore/10.2.0 7.0.31 GCCcore/10.3.0 7.0.31 GCCcore/11.2.0 7.0.31 GCCcore/11.3.0 7.0.31 GCCcore/12.3.0 7.0.31 GCCcore/13.2.0 7.0.31 GCCcore/6.3.0 7.0.31 GCCcore/6.4.0 7.0.31 GCCcore/7.3.0 7.0.31 GCCcore/8.3.0 7.0.31 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xskillscore/","title":"xskillscore","text":"xskillscore is an open source project and Python package that provides verification metrics of deterministic (and probabilistic from properscoring) forecasts with xarray.
homepage: https://xskillscore.readthedocs.io
version toolchain 0.0.26 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xtb-IFF/","title":"xtb-IFF","text":"General Intermolecular Force Field based on Tight-Binding Quantum Chemical Calculations.
homepage: https://github.com/grimme-lab/xtbiff
version toolchain 1.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xtb/","title":"xtb","text":"xtb - An extended tight-binding semi-empirical program package.
homepage: https://www.chemie.uni-bonn.de/pctc/mulliken-center/grimme/software/xtb
version versionsuffix toolchain 6.2.2-hotfix -Python-3.6.3 intel/2017b 6.2.3 foss/2019b 6.4.1 foss/2021b 6.4.1 intel/2021a 6.5.0 foss/2021b 6.5.1 foss/2022a 6.6.0 foss/2022a 6.6.0 intel/2022a 6.6.1 gfbf/2022b 6.6.1 gfbf/2023a 6.7.0 gfbf/2023a 6.7.1 gfbf/2023b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xtensor/","title":"xtensor","text":"xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions.
homepage: https://github.com/xtensor-stack/xtensor
version toolchain 0.24.0 foss/2021b 0.24.7 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xtrans/","title":"xtrans","text":"xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet.
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version toolchain 1.3.5 GCCcore/11.3.0 1.3.5 foss/2016a 1.3.5 gimkl/2.11.5 1.3.5 intel/2016a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xxHash/","title":"xxHash","text":"xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit.
homepage: https://cyan4973.github.io/xxHash
version toolchain 0.8.0 GCCcore/11.2.0 0.8.1 GCCcore/10.2.0 0.8.1 GCCcore/11.3.0 0.8.1 GCCcore/12.2.0 0.8.2 GCCcore/12.3.0 0.8.2 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/x/xxd/","title":"xxd","text":"xxd is part of the VIM package and serves to convert to/from hexdumps of binary files.
homepage: https://www.vim.org
version toolchain 8.2.4220 GCCcore/10.2.0 8.2.4220 GCCcore/10.3.0 8.2.4220 GCCcore/11.2.0 8.2.4220 GCCcore/11.3.0 9.0.1696 GCCcore/12.2.0 9.0.2112 GCCcore/12.3.0 9.1.0307 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/","title":"List of supported software (y)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- YACS
- Yade
- yaff
- Yambo
- yaml-cpp
- YANK
- YAPS
- Yasm
- YAXT
- yell
- yelp-tools
- yelp-xsl
- Yices
- YODA
- yt
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/YACS/","title":"YACS","text":"YACS was created as a lightweight library to define and manage system configurations, such as those commonly found in software designed for scientific experimentation. These \"configurations\" typically cover concepts like hyperparameters used in training a machine learning model or configurable model hyperparameters, such as the depth of a convolutional neural network.
homepage: https://github.com/rbgirshick/yacs
version toolchain 0.1.8 GCCcore/10.2.0 0.1.8 GCCcore/10.3.0 0.1.8 GCCcore/11.2.0 0.1.8 GCCcore/11.3.0 0.1.8 GCCcore/12.3.0 0.1.8 GCCcore/13.3.0 0.1.8 GCCcore/8.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/YANK/","title":"YANK","text":"A GPU-accelerated Python framework for exploring algorithms for alchemical free energy calculations
homepage: http://getyank.org/
version versionsuffix toolchain 0.25.2 -Python-3.8.2 intel/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/YAPS/","title":"YAPS","text":"YAPS - Yet Another Positioning Solver
homepage: https://github.com/baktoft/yaps
version versionsuffix toolchain 1.1.0 -R-3.5.1 foss/2018b 1.1.0 -R-3.6.0 intel/2019a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/YAXT/","title":"YAXT","text":"Yet Another eXchange Tool
homepage: https://www.dkrz.de/redmine/projects/yaxt
version toolchain 0.10.0 gompi/2022b 0.5.1 intel/2016b 0.5.1 intel/2017a 0.5.1 intel/2017b 0.6.0 intel/2018a 0.6.0 intel/2018b 0.6.0 iomkl/2018b 0.6.2 foss/2018b 0.6.2 gompi/2019b 0.6.2 iimpi/2019b 0.9.0 gompi/2020b 0.9.1 gompi/2021a 0.9.2 iimpi/2021b 0.9.2.1 gompi/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/YODA/","title":"YODA","text":"Yet more Objects for (High Energy Physics) Data Analysis
homepage: https://yoda.hepforge.org/
version toolchain 1.9.7 GCC/11.3.0 1.9.9 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/Yade/","title":"Yade","text":"Yade is an extensible open-source framework for discrete numerical models, focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, allowing independent implementation of new alogrithms and interfaces. Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging.
homepage: https://yade-dem.org/doc/
version versionsuffix toolchain 1.20.0 -Python-2.7.11 foss/2016a 1.20.0 -Python-2.7.11 intel/2016a 2016.06a -Python-2.7.12 foss/2016b 2016.06a -Python-2.7.12 intel/2016b 2017.01a -Python-2.7.12 intel/2016b 2018.02b -Python-2.7.14 intel/2018a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/Yambo/","title":"Yambo","text":"Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.
homepage: http://www.yambo-code.org
version toolchain 3.4.2 intel/2016.02-GCC-4.9 5.0.4 intel/2021a 5.1.2 intel/2021b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/Yasm/","title":"Yasm","text":"Yasm: Complete rewrite of the NASM assembler with BSD license
homepage: https://www.tortall.net/projects/yasm/
version toolchain 1.3.0 GCCcore/10.2.0 1.3.0 GCCcore/10.3.0 1.3.0 GCCcore/11.2.0 1.3.0 GCCcore/11.3.0 1.3.0 GCCcore/12.2.0 1.3.0 GCCcore/12.3.0 1.3.0 GCCcore/13.2.0 1.3.0 GCCcore/13.3.0 1.3.0 GCCcore/6.4.0 1.3.0 GCCcore/7.3.0 1.3.0 GCCcore/8.2.0 1.3.0 GCCcore/8.3.0 1.3.0 GCCcore/9.3.0 1.3.0 foss/2016a 1.3.0 foss/2016b 1.3.0 foss/2017a 1.3.0 gimkl/2.11.5 1.3.0 gimkl/2017a 1.3.0 intel/2016a 1.3.0 intel/2016b 1.3.0 intel/2017a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/Yices/","title":"Yices","text":"Yices 2 is an SMT solver that decides the satisfiability of formulas containing uninterpreted function symbols with equality, real and integer arithmetic, bitvectors, scalar types, and tuples. Yices 2 supports both linear and nonlinear arithmetic.
homepage: https://yices.csl.sri.com/index.html
version toolchain 2.6.2 GCCcore/10.2.0 2.6.4 GCCcore/12.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/yaff/","title":"yaff","text":"Yaff stands for 'Yet another force field'. It is a pythonic force-field code.
homepage: http://molmod.github.io/yaff/
version versionsuffix toolchain 1.0.develop.2.15 -Python-2.7.12-HDF5-1.8.18 intel/2016b 1.1.2 -Python-2.7.13 intel/2017a 1.1.3 -Python-2.7.13 intel/2017a 1.4.2 -Python-2.7.14 foss/2018a 1.4.2 -Python-2.7.14 intel/2017b 1.4.2 -Python-3.6.3 intel/2017b 1.4.2 -Python-2.7.14 intel/2018a 1.4.5 -Python-2.7.15 intel/2018b 1.5.0 -Python-2.7.15 intel/2018b 1.5.0 -Python-3.7.2 intel/2019a 1.6.0 -Python-3.7.4 foss/2019b 1.6.0 -Python-3.8.2 foss/2020a 1.6.0 foss/2020b 1.6.0 foss/2023a 1.6.0 -Python-3.7.2 intel/2019a 1.6.0 -Python-3.7.4 intel/2019b 1.6.0 -Python-3.8.2 intel/2020a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/yaml-cpp/","title":"yaml-cpp","text":"yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec
homepage: https://github.com/jbeder/yaml-cpp
version toolchain 0.6.3 GCCcore/8.3.0 0.7.0 GCCcore/11.3.0 0.7.0 GCCcore/12.2.0 0.7.0 GCCcore/12.3.0 0.8.0 GCCcore/13.2.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/yell/","title":"yell","text":"Yell - Your Extensible Logging Library is a comprehensive logging replacement for Ruby.
homepage: https://github.com/rudionrails/yell
version toolchain 2.2.2 GCC/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/yelp-tools/","title":"yelp-tools","text":"yelp-tools is a collection of scripts and build utilities to help create, manage, and publish documentation for Yelp and the web. Most of the heavy lifting is done by packages like yelp-xsl and itstool. This package just wraps things up in a developer-friendly way.
homepage: https://gitlab.gnome.org/GNOME/yelp-tools
version toolchain 42.1 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/yelp-xsl/","title":"yelp-xsl","text":"yelp-xsl is a collection of programs and data files to help you build, maintain, and distribute documentation. It provides XSLT stylesheets that can be built upon for help viewers and publishing systems. These stylesheets output JavaScript and CSS content, and reference images provided by yelp-xsl. This package also redistributes copies of the jQuery and jQuery.Syntax JavaScript libraries.
homepage: https://gitlab.gnome.org/GNOME/yelp-xslg
version toolchain 42.1 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/y/yt/","title":"yt","text":"yt is an open-source, permissively-licensed python package for analyzing and visualizing volumetric data.
homepage: https://yt-project.org
version toolchain 4.3.0 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/","title":"List of supported software (z)","text":"(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
- Z3
- z5py
- zarr
- Zeo++
- ZeroMQ
- zeus-mcmc
- zfp
- Zgoubi
- ZIMPL
- zingeR
- Zip
- zlib
- zlib-ng
- zlibbioc
- Zoltan
- Zopfli
- ZPAQ
- zsh
- zstd
- zUMIs
(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/Z3/","title":"Z3","text":"Z3 is a theorem prover from Microsoft Research with support for bitvectors, booleans, arrays, floating point numbers, strings, and other data types. This module includes z3_solver, the Python interface of Z3.
homepage: https://github.com/Z3Prover/z3
version versionsuffix toolchain 4.10.2 -Python-3.10.4 GCCcore/11.3.0 4.10.2 GCCcore/11.3.0 4.12.2 -Python-3.10.8 GCCcore/12.2.0 4.12.2 GCCcore/12.2.0 4.12.2 GCCcore/12.3.0 4.13.0 GCCcore/13.2.0 4.13.0 GCCcore/13.3.0 4.8.10 -Python-3.8.6 GCCcore/10.2.0 4.8.10 GCCcore/10.2.0 4.8.11 -Python-3.9.5 GCCcore/10.3.0 4.8.11 GCCcore/10.3.0 4.8.12 -Python-3.9.6 GCCcore/11.2.0 4.8.12 GCCcore/11.2.0 4.8.16 -Python-3.10.4 GCCcore/11.3.0 4.8.16 GCCcore/11.3.0 4.8.9 GCCcore/8.3.0 4.8.9 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/ZIMPL/","title":"ZIMPL","text":"ZIMPL is a little language to translate the mathematical model of a problem into a linear or nonlinear (mixed-) integer mathematical program expressed in .lp or .mps file format which can be read and (hopefully) solved by a LP or MIP solver.
homepage: https://zimpl.zib.de/
version toolchain 3.3.4 GCCcore/11.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/ZPAQ/","title":"ZPAQ","text":"zpaq is a free and open source (GPL v3) incremental, journaling command-line archiver for Windows, Linux and Mac OS/X
homepage: http://mattmahoney.net/dc/zpaq.html
version toolchain 7.00 GCC/4.8.2 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/Zeo%2B%2B/","title":"Zeo++","text":"Zeo++ is a software package for analysis of crystalline porous materials. Zeo++ can be used to perform geometry-based analysis of structure and topology of the void space inside a material, to assemble or alternate structures as well as to generate structure representations to be used in structure similarity calculations. Zeo++ can be used to either analyze a single structure or perform high-throughput analysis of a large database.
homepage: https://www.zeoplusplus.org/
version toolchain 0.3 intel-compilers/2023.1.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/ZeroMQ/","title":"ZeroMQ","text":"ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems.
homepage: http://www.zeromq.org/
version toolchain 4.1.4 foss/2016a 4.1.4 intel/2016a 4.1.5 intel/2016b 4.2.0 foss/2016b 4.2.0 intel/2016b 4.2.2 foss/2017a 4.2.2 foss/2017b 4.2.2 fosscuda/2017b 4.2.2 intel/2017a 4.2.2 intel/2017b 4.2.2 intelcuda/2017b 4.2.5 foss/2018a 4.2.5 foss/2018b 4.2.5 fosscuda/2018b 4.2.5 intel/2018a 4.2.5 intel/2018b 4.3.2 GCCcore/8.2.0 4.3.2 GCCcore/8.3.0 4.3.2 GCCcore/9.3.0 4.3.3 GCCcore/10.2.0 4.3.4 GCCcore/10.3.0 4.3.4 GCCcore/11.2.0 4.3.4 GCCcore/11.3.0 4.3.4 GCCcore/12.2.0 4.3.4 GCCcore/12.3.0 4.3.5 GCCcore/13.2.0 4.3.5 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/Zgoubi/","title":"Zgoubi","text":"Zgoubi is a ray-tracing code in use for charged particle beam dynamics simulations. It can simulate beam dynamics in a large variety of machines and optical systems.
homepage: https://zgoubi.sourceforge.io
version toolchain 6.0.2 GCCcore/10.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/Zip/","title":"Zip","text":"Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives have been portability and other-than-MSDOS functionality
homepage: http://www.info-zip.org/Zip.html
version toolchain 3.0 GCCcore/10.2.0 3.0 GCCcore/10.3.0 3.0 GCCcore/11.2.0 3.0 GCCcore/11.3.0 3.0 GCCcore/12.2.0 3.0 GCCcore/12.3.0 3.0 GCCcore/13.2.0 3.0 GCCcore/13.3.0 3.0 GCCcore/7.3.0 3.0 GCCcore/8.2.0 3.0 GCCcore/8.3.0 3.0 GCCcore/9.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/Zoltan/","title":"Zoltan","text":"Zoltan Dynamic Load Balancing and Graph Algorithm Toolkit
homepage: https://sandialabs.github.io/Zoltan/
version toolchain 3.901 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/Zopfli/","title":"Zopfli","text":"Zopfli Compression Algorithm is a compression library programmed in C to perform very good, but slow, deflate or zlib compression.
homepage: https://github.com/google/zopfli
version toolchain 1.0.3 GCCcore/10.2.0 1.0.3 GCCcore/10.3.0 1.0.3 GCCcore/11.3.0 1.0.3 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/z5py/","title":"z5py","text":"Lightweight C++ and Python interface for datasets in zarr and N5 format.
homepage: https://github.com/constantinpape/z5/
version toolchain 2.0.17 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/zUMIs/","title":"zUMIs","text":"A fast and flexible pipeline to process RNA sequencing data with UMIs.
homepage: https://github.com/sdparekh/zUMIs
version versionsuffix toolchain 2.9.7 -R-4.3.2 foss/2023a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/zarr/","title":"zarr","text":"Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing.
homepage: https://zarr.readthedocs.io/en/stable/
version versionsuffix toolchain 2.1.4 -Python-2.7.13 foss/2017a 2.10.1 foss/2021a 2.13.3 foss/2021b 2.13.3 foss/2022a 2.16.0 foss/2022b 2.17.1 foss/2023a 2.4.0 -Python-3.8.2 foss/2020a 2.8.1 foss/2020b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/zeus-mcmc/","title":"zeus-mcmc","text":"Zeus is a Python implementation of the Ensemble Slice Sampling method.
homepage: https://zeus-mcmc.readthedocs.io
version toolchain 2.5.4 foss/2022a (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/zfp/","title":"zfp","text":"zfp is a compressed format for representing multidimensional floating-point and integer arrays. zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications that read and write large data sets to and from disk.
homepage: https://github.com/LLNL/zfp
version toolchain 0.5.5 GCCcore/10.2.0 1.0.0 GCCcore/10.3.0 1.0.0 GCCcore/11.3.0 1.0.0 GCCcore/9.3.0 1.0.1 GCCcore/12.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/zingeR/","title":"zingeR","text":"Zero-Inflated Negative binomial Gene Expression in R
homepage: https://github.com/statOmics/zingeR
version versionsuffix toolchain 20180131 -R-3.5.1 foss/2018b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/zlib-ng/","title":"zlib-ng","text":"zlib data compression library for the next generation systems
homepage: https://github.com/zlib-ng/zlib-ng
version toolchain 2.0.5 GCCcore/10.2.0 2.0.6 GCCcore/10.3.0 2.0.7 GCCcore/11.3.0 2.1.6 GCCcore/12.3.0 2.2.1 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/zlib/","title":"zlib","text":"zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.
homepage: http://www.zlib.net/
version toolchain 1.2.10 system 1.2.11 GCCcore/10.1.0 1.2.11 GCCcore/10.2.0 1.2.11 GCCcore/10.3.0 1.2.11 GCCcore/11.1.0 1.2.11 GCCcore/11.2.0 1.2.11 GCCcore/5.4.0 1.2.11 GCCcore/5.5.0 1.2.11 GCCcore/6.3.0 1.2.11 GCCcore/6.4.0 1.2.11 GCCcore/7.1.0 1.2.11 GCCcore/7.2.0 1.2.11 GCCcore/7.3.0 1.2.11 GCCcore/7.4.0 1.2.11 GCCcore/8.1.0 1.2.11 GCCcore/8.2.0 1.2.11 GCCcore/8.3.0 1.2.11 GCCcore/8.4.0 1.2.11 GCCcore/9.1.0 1.2.11 GCCcore/9.2.0 1.2.11 GCCcore/9.3.0 1.2.11 GCCcore/9.4.0 1.2.11 GCCcore/system 1.2.11 gimkl/2017a 1.2.11 system 1.2.12 GCCcore/11.3.0 1.2.12 GCCcore/12.1.0 1.2.12 GCCcore/12.2.0 1.2.12 GCCcore/9.5.0 1.2.12 system 1.2.13 GCCcore/11.4.0 1.2.13 GCCcore/12.3.0 1.2.13 GCCcore/13.1.0 1.2.13 GCCcore/13.2.0 1.2.13 system 1.2.7 GCC/4.8.1 1.2.7 GCC/4.8.2 1.2.8 GCC/4.8.2 1.2.8 GCC/4.8.3 1.2.8 GCC/4.8.4 1.2.8 GCC/4.9.2-binutils-2.25 1.2.8 GCC/4.9.2 1.2.8 GCC/4.9.3-2.25 1.2.8 GCC/4.9.3-binutils-2.25 1.2.8 GCC/4.9.3 1.2.8 GCC/5.1.0-binutils-2.25 1.2.8 GCCcore/4.9.2 1.2.8 GCCcore/4.9.3 1.2.8 GCCcore/4.9.4 1.2.8 GCCcore/5.3.0 1.2.8 GCCcore/5.4.0 1.2.8 GCCcore/6.1.0 1.2.8 GCCcore/6.2.0 1.2.8 GCCcore/6.3.0 1.2.8 GNU/4.9.3-2.25 1.2.8 foss/2016.04 1.2.8 foss/2016a 1.2.8 gimkl/2.11.5 1.2.8 intel/2016.02-GCC-4.9 1.2.8 intel/2016a 1.2.8 intel/2016b 1.2.8 intel/2017.01 1.2.8 iomkl/2016.07 1.2.8 iomkl/2016.09-GCC-4.9.3-2.25 1.2.8 system 1.3.1 GCCcore/13.3.0 1.3.1 GCCcore/14.1.0 1.3.1 GCCcore/14.2.0 1.3.1 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/zlibbioc/","title":"zlibbioc","text":"This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means.
homepage: https://bioconductor.org/packages/release/bioc/html/zlibbioc.html
version versionsuffix toolchain 1.18.0 -R-3.2.3 intel/2016a 1.20.0 -R-3.3.1 intel/2016b (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/zsh/","title":"zsh","text":"Zsh is a shell designed for interactive use, although it is also a powerful scripting language.
homepage: http://www.zsh.org/
version toolchain 5.1.1 GNU/4.9.3-2.25 5.2 foss/2016b 5.8 GCC/8.3.0 5.8 system 5.9 system (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5},{"location":"version-specific/supported-software/z/zstd/","title":"zstd","text":"Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.
homepage: https://facebook.github.io/zstd
version toolchain 1.3.4 foss/2016b 1.4.0 GCCcore/7.3.0 1.4.0 GCCcore/8.2.0 1.4.0 foss/2018b 1.4.4 GCCcore/8.3.0 1.4.4 GCCcore/9.3.0 1.4.5 GCCcore/10.2.0 1.4.9 GCCcore/10.3.0 1.5.0 GCCcore/11.2.0 1.5.2 GCCcore/11.3.0 1.5.2 GCCcore/12.2.0 1.5.5 GCCcore/12.3.0 1.5.5 GCCcore/13.2.0 1.5.6 GCCcore/13.3.0 (quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)
","boost":0.5}]}
\ No newline at end of file
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Use the menu to navigate, or use the search feature (top right).
See also the EasyBuild tutorial (separate website).
To contribute to this documentation, open a pull request.
Quick links
- What is EasyBuild? | Terminology
- Installing, configuring, and using EasyBuild
- Writing easyconfig files | available easyconfig parameters
- Generic easyblocks
- List of common toolchains and supported software
- Contributing to EasyBuild | GitHub integration features
- EasyBuild release notes | EasyBuild v5.0
- For end users | user support | contributors | developers | maintainers
- Getting help: mailing list - Slack - conference calls - GitHub
(last update: 2024-12-24 - easybuild-docs commit dff7bc73e)
"},{"location":"archived-easyconfigs/","title":"Archived easyconfigs","text":"Since EasyBuild v3.0.0, easyconfig files using deprecated (i.e., old and inactive) toolchains are archived.
"},{"location":"archived-easyconfigs/#archived_easyconfigs_toolchain_deprecation","title":"Toolchain deprecation","text":"Once in a blue moon, we review the list of toolchains (& versions) that are included in EasyBuild.
Easyconfig files that use toolchains that become deprecated are then moved to the easyconfigs archive, i.e. the __archive__ subdirectory in the easybuild-easyconfigs repository (see https://github.com/easybuilders/easybuild-easyconfigs/tree/main/easybuild/easyconfigs/__archive__).
"},{"location":"archived-easyconfigs/#archived_easyconfigs_deprecated_toolchains_what","title":"What are deprecated toolchains?","text":"Toolchains become deprecated if:
- no easyconfig files using that toolchain have been contributed recently (e.g., in the last year)
- that toolchain is considered to be inactive, after consulting the EasyBuild community (via mailing list, bi-weekly conf calls)
Deprecating a toolchain implies that all easyconfigs using that toolchain are moved to the easyconfigs archive, and that they are no longer included in the EasyBuild regression test. In addition, these easyconfigs are 'hidden' from plain sight, in the sense that you need to use --consider-archived-easyconfigs to make EasyBuild consider them when it is looking for easyconfigs (e.g., with --search or --robot).
This does not mean that the support for using these toolchains is removed from the EasyBuild framework, although not testing them anymore may imply that using them may no longer work at some point in time.
For toolchains for which no active versions are available (outside of the easyconfigs archive), it is possible that they will be reactivated, if a new toolchain version is contributed.
"},{"location":"archived-easyconfigs/#archived_easyconfigs_deprecated_toolchains_why","title":"Why are toolchains being deprecated?","text":" - using old toolchains (incl. old compilers and/or libraries) is likely to become more and more difficult on modern operating systems
- these toolchains put a significant burden on the regression testing for EasyBuild releases
- easyconfigs using old toolchains are likely to be for old software versions, which may no longer be relevant anyway
"},{"location":"archived-easyconfigs/#archived_easyconfigs_consider","title":"Using --consider-archived-easyconfigs","text":"To make EasyBuild consider archived easyconfig files, you need to enable the --consider-archived-easyconfigs configuration option:
While regenerating existing module files, you may want to preserve the existing module files to compare and assess that the changes in the newly generated module file match expectations.
Backups are stored in the same directory as where the module file was located, and the files are given an additional extension of the form .bak_<year><month><day><hour><min><sec>.
The location of the backed up module file will be printed, as well as a \"unified diff\" comparison (very similar to what diff -u produces) between the backed up module file and the newly generated module file (or a message mentioning that no differences were found).
"},{"location":"backup-modules/#backup_modules_disable","title":"Disabling automatic backup of modules","text":"Cleaning up the backup module files can be done with the following command (for example):
The code style we follow in the EasyBuild code repository is mainly dictated by the Python standard PEP8.
The only (major) exception to PEP8 is our preference for longer line lengths: line lengths must be limited to 120 characters, and should by preference be shorter than 100 characters (as opposed to the 80-character limit in PEP8).
"},{"location":"code-style/#notes","title":"Notes","text":"This page documents the concept of common toolchains in the EasyBuild community; for a more general definition of what (compiler) toolchains are, see Toolchains.
"},{"location":"common-toolchains/#common_toolchains_what","title":"Definition and motivation","text":"Picking a compiler toolchain to use is one of the first things you (need to) do when starting to use EasyBuild. This can be a daunting task, since a whole bunch of toolchains and different toolchain versions are readily available in EasyBuild. It may be difficult to determine which toolchain would be most rewarding to use, in terms of stability, performance of the resulting binaries and readily available easyconfig files.
In an attempt to focus the effort of the EasyBuild community, the concept of so-called common toolchains was introduced.
The idea is to compose and maintain a limited set of specific compiler toolchains, and try and convince many HPC sites to employ these toolchains. This helps in assuring stability of these toolchains w.r.t. which software can be built (correctly) with them, since they get significantly more testing. In addition, the expectation/hope is that more easyconfigs are contributed back to the central easyconfigs repository (https://github.com/easybuilders/easybuild-easyconfigs), resulting in a wide range of readily available easyconfig files using the common toolchains.
The intention is to revise/update the definitions of the common toolchains regularly (see Update cycle for common toolchains), which again can be a joint effort that benefits many HPC sites.
To be more helpful in understanding the differences between these families, here is a diagram that explains what is added in each additional layer.
Note: because there have been a few changes in toolchains, there are notes below the diagram that explain the differences between the generations going back to the 2020b version of the foss and intel toolchains.
"},{"location":"common-toolchains/#newest-generations-2022b-and-later","title":"Newest generations (Keep in mind that when creating an Easyconfig, you need to look at what toolchain \"level\" (e.g. foss vs GCC) your dependencies are using and choose the highest of them (or higher if needed) for your easyconfig. For example, if one of your dependencies is using the foss toolchain, you need to use the foss toolchain, and not the GCC toolchain.
"},{"location":"common-toolchains/#common_toolchains_foss","title":"The toolchain name was deliberately chosen to be generic, to allow for swapping any of the toolchain components with a better (open source) alternative in the future, should the need or opportunity arise.
"},{"location":"common-toolchains/#common_toolchains_intel","title":"This compiler toolchain includes licensed software; valid licenses must be available to install and use it.
"},{"location":"common-toolchains/#common_toolchains_versioning_scheme","title":"Versioning scheme for common toolchains","text":"The common toolchains follow a specific versioning scheme, which takes the 6-month update cycle into account.
Each revision of the common toolchains is versioned as the year in which it was defined, plus an additional 'a' or 'b' to indicate whether the toolchain was defined at the start of the year ('a') or halfway through the year ('b'); in short, the common toolchains are versioned as <year>{a,b}.
These versions are not considered to be part of the series of common toolchains (even though they consists of the same toolchain components). These versions may be site-specific, or compositions that were put in place to evaluate a potential future common toolchain.
The intention is to revise and update the common toolchains every 6 months: once in late December/early January (version <year>a), and once in late June/early July (version <year>b).
This is meant be to be a community effort, in the sense that a proposal for an updated composition is shared and discussed before it is set in stone.
Recent versions of each of the toolchain components are considered, taking into account stability, performance improvements, added features, known bugs/issues and experiences with those versions.
Moreover, the proposed toolchain compositions are tested extensively, typically by rebuilding all available easyconfigs that are using the most recent revision of the common toolchains at that time.
"},{"location":"common-toolchains/#common_toolchains_overview","title":"Overview of common toolchains","text":""},{"location":"common-toolchains/#common_toolchains_overview_foss","title":"Component versions in Sometimes the need arises to customize one or more components of a common toolchain w.r.t. site-specific aspects. One common example is using additional configuration options for Open MPI.
To customize a toolchain component, you should copy the corresponding easyconfig file, modify according to your needs, and make sure it is included in a location in the robot search path that precedes the location of the easyconfig files that are included with EasyBuild (see also Searching for easyconfigs: the robot search path), before building and installation the toolchain.
"},{"location":"common-toolchains/#more-information-about-toolchains","title":"More information about toolchains","text":"Please see the List of known toolchains for how to obtain a listing of the currently known toolchains.
For a detailed listing of the compiler options available with each toolchain, please see Available toolchain options (by toolchain).
"},{"location":"configuration/","title":"Configuring EasyBuild","text":"This page discusses the recommended style of configuring EasyBuild, which is supported since EasyBuild v1.3.0.
See a demo on configuring EasyBuild.
"},{"location":"configuration/#configuration_types","title":"Supported configuration types","text":"Of course, combining any of these types of configuration works too (and is even fairly common).
The order of preference for the different configuration types is as listed above, that is:
Note that the various available configuration options are handled consistently across the supported configuration types.
For example: to configure EasyBuild to use Lmod as modules tool, the following alternatives are available:
For more details w.r.t. each of the supported configuration types, see below.
"},{"location":"configuration/#configuration_file","title":"Configuration file(s)","text":""},{"location":"configuration/#list_of_configuration_files","title":"List of used configuration files","text":"The list of configuration files that will be used by EasyBuild is determined in the following order of preference:
By default, EasyBuild will use existing configuration files at the following paths:
If multiple configuration files are listed via a mechanism listed above, the settings in the last configuration file have preference over the others.
Each available configuration file will be used, and the configuration settings specified in these files will be retained according to the order of preference as indicated above: settings in configuration files specified via --configfiles override those in configuration files specified via $EASYBUILD_CONFIGFILES, which in turns override settings in default configuration files.
"},{"location":"configuration/#ignored-configuration-files","title":"Ignored configuration files","text":"The EasyBuild configuration file follows the default Python configuration format as parsed by the configparser module (see https://docs.python.org/3/library/configparser.html).
Configuration files are organized in sections, the section name for a particular configuration setting is indicated in the output of eb --help. Some examples sections are: MAIN, basic, config, informative, override, regtest, software, unittest, etc.
Sections are indicated by specifying the section name in square brackets on a dedicated line, e.g., [basic].
An example configuration file that should make everything clear is shown below.
These template values are only supported in configuration files, not in environment variable values or command line option values.
Using an unknown template value, i.e. either one for a configuration option that was not defined in the configuration file, or a non-existing one for a particular default value, will result in an error like: ConfigParser.InterpolationMissingOptionError: Bad value substitution.
"},{"location":"configuration/#example","title":"Example","text":"To include both the (custom) location for the easyconfigs archive repository and the default list of robot search paths in the active robot search path, the following configuration file entry can be used, featuring the template for the repositorypath configuration option and the provided DEFAULT_ROBOT_PATHS constant::
See also Controlling the robot search path.
"},{"location":"configuration/#generating-a-template-configuration-file","title":"Generating a template configuration file","text":"Configuration settings specified this way always override the corresponding setting specified in a configuration file.
More examples of using environment variables to configure EasyBuild are shown in the sections below.
Any configuration option of EasyBuild which can be tuned by command line or via the configuration file, can also be tuned via a corresponding environment variable.
For some configuration options, both short and long command line arguments are available (see eb --help); the long options indicate how the configuration setting should be specified in a configuration file or via an environment variable ($EASYBUILD_<LONGOPTION>).
To get an overview of the current EasyBuild configuration across all configuration types, you can use eb --show-config.
For a full overview of the current configuration, including all configuration settings, see eb --show-full-config.
"},{"location":"configuration/#configuration_available_settings","title":"Available configuration settings","text":"A couple of selected configuration settings are discussed below, in particular the mandatory settings.
"},{"location":"configuration/#configuration_mandatory_settings","title":"Mandatory configuration settings","text":"A handful of configuration settings are mandatory, and should be provided using one of the supported configuration types.
The following configuration settings are currently mandatory (more details in the sections below):
If any of these configuration settings is not provided in one way or another, EasyBuild will complain and exit.
Note that these locations are also used when EasyBuild looks for patch files in addition to the various easybuild/easyconfigs directories that are listed in the $PYTHONPATH.
Note that the build directories are emptied and removed by EasyBuild when the installation is completed (by default).
There are several ways in which the software and modules install path used by EasyBuild can be configured:
These configuration options have precedence over all of the other configuration options that relate to specifying the install path for software and/or modules (see below).
"},{"location":"configuration/#parent_installpath","title":"Parent install path: The install path for software and modules specifically is determined by combining --installpath with --subdir-software, and combining --installpath with --subdir-modules and --suffix-modules-path, respectively.
For more information on these companion configuration options, see Software and modules install path subdirectories (--subdir-software, --subdir-modules, --suffix-modules-path).
"},{"location":"configuration/#full-install-path-for-software-and-module-file","title":"Full install path for software and module file","text":"The full software and module install paths for a particular software package are determined by the active module naming scheme along with the general software and modules install paths specified by the EasyBuild configuration.
Both the software itself and the corresponding module file will be installed in a subdirectory of the corresponding install path named according to the active module naming scheme (default format: <name>/<version>-<toolchain><versionsuffix>). Additionally, symlinks to the actual module file are installed in a subdirectory of the modules install path named according to the value of the moduleclass easyconfig parameter.
For more information on the module naming scheme used by EasyBuild, see Active module naming scheme (--module-naming-scheme).
"},{"location":"configuration/#updating-modulepath","title":"Updating Or, optionally an extra argument representing a subdirectory can be specified, e.g.:
You do not have to worry about importing these classes, EasyBuild will make them available to the configuration file.
If access to the easyconfigs repository fails for some reason (e.g., no network or a missing required Python module), EasyBuild will issue a warning. The software package will still be installed, but the (successful) easyconfig will not be automatically added to the archive (i.e., it is not considered a fatal error).
"},{"location":"configuration/#logfile_format","title":"Logfile format (Because templating is supported in configuration files themselves (see Templates and constants supported in configuration files), the '%' character in these template values must be escaped when used in a configuration file (and only then), e.g., '%%(name)s'. Without escaping, an error like InterpolationMissingOptionError: Bad value substitution will be thrown by ConfigParser.
For example, configuring EasyBuild to generate a log file mentioning only the software name in a directory named easybuild can be done via the --logfile-format command line option:
or by including the following in an EasyBuild configuration file (note the use of '%%' to escape the name template value here):
The subsections below discuss a couple of commonly used optional configuration settings.
"},{"location":"configuration/#prefix","title":"Overall prefix path (Specifying the modules tool that should be used by EasyBuild can be done using the modules-tool configuration setting. A list of supported modules tools can be obtained using eb --avail-modules-tools.
The module naming scheme that should be used by EasyBuild can be specified using the module-naming-scheme configuration setting.
For more details, see the dedicated page on using a custom module naming scheme.
"},{"location":"configuration/#module_syntax","title":"Module files syntax (Lmod is able to deal with having module files in place in both Tcl and Lua syntax. When a module file in Lua syntax (i.e., with a .lua file name extension) is available, a Tcl module file with the same name will be ignored. The Tcl-based environment modules tool will simply ignore module files in Lua syntax, since they do not contain the header string that is included in Tcl module files.
Using module files in Lua syntax has the advantage that Lmod does not need to translate from Lua to Tcl internally when processing the module files, which benefits responsiveness of Lmod when used interactively by users. In terms of Lmod-specific aspects of module files, the syntax of the module file does not matter; Lmod-specific statements supported by EasyBuild can be included in Tcl module files as well, by guarding them by a condition that only evaluates positively when Lmod is consuming the module file, i.e. 'if { [ string match \"*tcl2lua.tcl\" $env(_) ] } { ... }'. Only conditional load statements like 'load(atleast(\"gcc\",\"4.8\"))' can only be used in Lua module files.
"},{"location":"containers/","title":"Generating container recipes & images","text":"EasyBuild has support for generating Singularity and Docker container recipes which will use EasyBuild to build and install a specified software stack. In addition, EasyBuild can (optionally) leverage the build tool provided by the container software of choice to create container images.
The features documented here have been available since EasyBuild v3.6.0 but are still experimental, which implies they are subject to change in upcoming versions of EasyBuild.
See Experimental features for more information.
Initially (since EasyBuild v3.6.0), only Singularity (https://www.sylabs.io/singularity) was supported. Since EasyBuild v3.6.2, generating (recipes for) Docker (https://www.docker.com/) containers is also supported.
In EasyBuild v3.9.2 the support for generating Singularity container recipes/images was enhanced significantly.
"},{"location":"containers/#containers_req","title":"Requirements","text":"The resulting container recipe will, in turn, leverage EasyBuild to build and install the software that corresponds to the easyconfig files that are specified as arguments to the eb command (and all required dependencies, if needed).
EasyBuild will refuse to overwrite existing container recipes.
When generating container recipes, EasyBuild will replace the following template values:
For more details on the last three, see Linux distro bootstrap agents.
Specifying any unknown keywords will results in an error.
"},{"location":"containers/#container_bootstrap_agent_image_based","title":"Image-based bootstrap agents","text":"(e.g. docker, library, localimage, shub)
These bootstrap agents involve using an existing container image as a base.
Each of the other image-based bootstrap agents imply that the container image to use as a base is downloaded from the corresponding registry, ad specified through the from keyword, with a specific format:
For more details, see https://www.sylabs.io/guides/latest/user-guide/appendix.html#build-modules.
"},{"location":"containers/#containers_usage_container_base_image_requirements","title":"Requirements for base container image","text":"The generated container recipe currently hardcodes some of this. We intend to make this more configurable in a future version of EasyBuild.
"},{"location":"containers/#container_bootstrap_agent_linux_distro","title":"Linux distro bootstrap agents","text":"(e.g. arch, busybox, debootstrap, yum, zypper)
Dedicated bootstrap agents are supported for different flavors of Linux distributions, including:
When one of these bootstrap agents is used, additional keywords can be specified:
See also https://www.sylabs.io/guides/latest/user-guide/appendix.html#yum-bootstrap-agent and https://www.sylabs.io/guides/latest/user-guide/appendix.html#zypper-bootstrap-agent.
"},{"location":"containers/#container_bootstrap_agent_linux_distro_mirrorurl","title":"To instruct EasyBuild to also build a container image from the generated container recipe, use --container-build-image (in combination with -C or --containerize).
EasyBuild will leverage functionality provided by the container software of choice (see Type of container recipe/image to generate) to build the container image.
In order to leverage the image building functionality of the container software, admin privileges are typically required. Therefore, EasyBuild will run the command to build the container image with sudo. You may need to enter your password to let the command execute.
If you're not comfortable with this, you can just let EasyBuild generate the container recipe, and then use that to build the actual container images yourself, either locally or through Singularity Hub (https://singularity-hub.org).
When building container images, make sure to use a file system location with sufficient available storage space. Singularity may pull metadata during the build, and each image can range from several hundred MBs to GBs, depending on software stack you are including in the container image.
EasyBuild will refuse to overwrite existing container images.
Docker supports a limited set of the container options. Example of commands that can be used to generate Docker containers are:
Below is an example of container recipe for that was generated by EasyBuild, using the following command:
In addition, the generated module files will follow the default module naming scheme (EasyBuildMNS). The modules that correspond to the easyconfig files that were specified on the command line will be loaded automatically, see the statements in the %environment section of the generated container recipe.
"},{"location":"containers/#containers_example_build_image","title":"Example of building container image","text":"To control the location where EasyBuild will put generated container recipes & images, use the --containerpath configuration setting. Next to providing this as an option to the eb command, you can also define the $EASYBUILD_CONTAINERPATH environment variable or specify containerpath in an EasyBuild configuration file.
The format for container images that EasyBuild is produces via the functionality provided by the container software can be controlled via the --container-image-format configuration setting.
For Singularity containers (see Type of container recipe/image to generate), three image formats are supported:
See also https://www.sylabs.io/guides/latest/user-guide/build_a_container.html .
"},{"location":"containers/#containers_cfg_image_name","title":"Name for container recipe & image","text":"By default, EasyBuild will use the name of the first easyconfig file (without the .eb suffix) as a name for both the container recipe and image.
The container software that EasyBuild leverages to build container images may be using a temporary directory in a location that doesn't have sufficient free space.
To avoid long build times and excessive large container images, you can construct your target container image step-by-step, by first building a base container image for the compiler toolchain you want to use, and then using it to build a container images for a particular (set of) software package(s).
In some cases, you may need to \"seed in\" manually downloaded source files into the container build environment, because the sources can not be downloaded automatically.
As shown in Example of a generated container recipe, the container recipe generated by EasyBuild includes /tmp/easybuild/sources/ as a fallback directory in the list of locations considered by EasyBuild when looking for sources/patches (see also Source path).
That way, you can copy source files that should be available when building the container image into /tmp/easybuild/sources/.
"},{"location":"contributing/","title":"Contributing","text":"This documentation explains how you can contribute to EasyBuild, and discusses the review process for contributions.
"},{"location":"contributing/#contributing_how","title":"How to contribute","text":"It is a common misconception that contributing to an open source project requires being intimately familiar with its codebase.
There are various ways to contribute, even if you don't have any experience with the programming language(s) being used by the project you are interested in.
An easy way to contribute to EasyBuild, even without having a lot of hands-on experience with it, is to provide feedback on your experiences.
Feedback from people new to EasyBuild is valuable, since it provides a perspective that is easily overlooked by more experienced users.
If you run into unexpected problems when using EasyBuild, please open a bug report in the issue tracker of the relevant GitHub repository:
If you have suggestions for enhancements or ideas for new features that could be useful, please open an issue in the relevant GitHub repository (see Reporting bugs).
Describe what you have in mind, and maybe also provide a concrete example to illustrate how your suggestion would improve the current functionality.
"},{"location":"contributing/#contributing_helping_others","title":"Helping others","text":"Try and help others based on your experience, or help them figure out an answer to their question or a solution to their problem using the EasyBuild documentation or by reaching out to someone else in the EasyBuild community that may know the answer.
The EasyBuild community is known to be very welcoming and helpful, and you too can be a part of that.
"},{"location":"contributing/#contributing_easyconfigs","title":"Contributing easyconfig files","text":"This includes easyconfigs for software that is not supported yet by EasyBuild, as well as updates to existing easyconfigs (e.g., version updates, using a different toolchain, etc.), even if you consider the updates to be trivial. Keep in mind that being able to use something that is known to work out-of-the-box can save quite a bit of time compared to having to tweak existing easyconfigs and validate the result installations.
Of course you can also contribute code changes, including bug fixes, enhancements or additional features in the EasyBuild framework, the easyblocks repository, the test suites or in related scripts.
Do keep in mind that this requires some experience with Python, although you should be able to go a long way by using the existing code base as support.
See Pull requests for more information on the practical aspects of contributing code.
"},{"location":"contributing/#contributing_docs","title":"Writing documentation","text":"Another way to contribute to EasyBuild without having to implement Python code is by writing documentation, i.e. enhancing or updating existing documentation or documenting features that are not covered yet.
To contribute to the documentation hosted at https://docs.easybuild.io, you should open a pull request to the main branch of the https://github.com/easybuilders/easybuild-docs repository; see the docs subdirectory.
The EasyBuild documentation is made with Material for MkDocs and written in MarkDown.
"},{"location":"contributing/#contributing_conversation","title":"Joining the conversation","text":"Last but not least, you can actively join the conversation that arise on the EasyBuild mailing list, the #easybuild IRC channel and during the bi-weekly EasyBuild conference calls (see https://github.com/easybuilders/easybuild/wiki/Conference-calls).
Engage with the EasyBuild community, and help steer EasyBuild development by participating in the conversations regarding a variety of topics related to building and installing (scientific) software.
"},{"location":"contributing/#contributing_pull_requests","title":"Pull requests","text":"To contribute to the EasyBuild framework, easyblocks, easyconfig files or the EasyBuild documentation, you will need to open a pull request to the corresponding GitHub repository:
However, this can be largely circumvented by using the GitHub integration provided by EasyBuild, see Integration with GitHub .
"},{"location":"contributing/#contributing_pull_request_setup","title":"Setting up","text":"These instructions assume that you already have a working GitHub account.
If you don't have a GitHub account yet, visit https://github.com/ to create one.
We highly recommend registering your SSH public key in your GitHub account, via https://github.com/settings/keys. This allows pushing to your fork of the GitHub repositories without using a password.
Before you can open pull requests, you will need to fork the GitHub repository you are targeting, and create a local working copy of that repository. This only needs to be done once for every of the EasyBuild repositories.
However, the instructions are equivalent for the other EasyBuild repositories.
"},{"location":"contributing/#contributing_pull_request_setup_fork_repo","title":"Forking the repository","text":"You will have to use this fork as a staging area for your work, to prepare your contributions before creating the actual pull requests.
"},{"location":"contributing/#contributing_pull_request_setup_working_copy","title":"Creating a working copy","text":"In addition to forking the repository on GitHub, you also need to create a local working copy of the repository. This is basically a local checkout of the repository where you can track the changes you are making.
With this in place, you are all set to open pull requests for your contributions.
"},{"location":"contributing/#keeping-the-develop-branch-in-sync","title":"Keeping the This section describes the manual procedure to open a new pull request.
We assume you are already located in your local working copy of the repository you want to contribute to (e.g., easybuild-framework).
First, create a new branch for your work. You can do this either before or after making the changes that you would like to contribute, but we recommend to create a new branch before making any changes.
You can choose the branch name freely, but make it sufficiently descriptive \u2013 your future self will thank you.
"},{"location":"contributing/#contributing_creating_pull_requests_commit","title":"Committing your changes","text":"To 'save' your changes, you should create one or more commits in the branch you created. We recommended making separate commits for different 'units of work'.
First, make sure you have checked out the branch were you want to commit the changes to. For example, to prepare for committing changes to the mybranch branch:
Please use a concise commit message that describes the changes you made.
Once you have committed your changes to a branch, you should push your branch to your fork of the GitHub repository using git push.
The above command will make your work public.
"},{"location":"contributing/#contributing_creating_pull_requests_pr_title","title":"Pull request title & description","text":"Please use a descriptive (short) title for your pull requests, and clarify (if needed) in the pull request description.
For pull requests to the easyconfig repository, we recommend using this format for the pull request title when contributing new easyconfig files:
If you are opening a work-in-progress pull request, for example to solicit feedback, tag it using (WIP). in the pull request title.
"},{"location":"contributing/#contributing_creating_pull_requests_open_pr","title":"Opening the pull request","text":"To open a pull request using the branch you pushed, you should use the GitHub interface, and follow the steps outlined below.
Next, your pull request will be reviewed & tested, see Review process for contributions.
"},{"location":"contributing/#contributing_updating_pull_requests","title":"Updating existing pull requests","text":"This section describes the manual procedure to create a new pull request.
It is quite common to update a pull request after creating it, for example if the test suite run in GitHub Actions reports problems with the changes being made, or as a response to someone reviewing your contribution.
To update an existing pull request, it suffices to add commits to the branch that was used for opening the pull request, and pushing the updated branch to GitHub.
Updating a pull request will trigger GitHub Actions to re-test your contribution, and a notification will be sent out to whoever is 'watching' your pull request.
"},{"location":"contributing/#contributing_merging_pull_requests","title":"Merging of pull requests","text":"Once your pull request has been given the green light by GitHub Actions and one or more people reviewing have approved the changes, it can be merged into the develop branch.
This can only be done by a member of the EasyBuild maintainers team. Only pull requests that meet the requirements are eligible for merging, see Requirements for pull requests .
Merging a pull request usually implies that the changes will be part of the next EasyBuild release.
"},{"location":"contributing/#contributing_review_process","title":"Review process for contributions","text":"Each contribution is thoroughly reviewed and tested before it gets merged in. Some aspects of this are automated, others require human intervention.
"},{"location":"contributing/#contributing_review_process_pr_requirements","title":"Requirements for pull requests","text":"Only pull requests (PRs) that fulfil these requirements are eligible to be merged:
Occasionally, an additional version branch (e.g. 3.3.x) may be introduced temporarily, in case an intermittent bugfix release is being worked on.
"},{"location":"contributing/#contributing_review_process_github_actions","title":"Test suite (GitHub Actions)","text":"Each pull request is tested automatically by GitHub Actions and the test result is reported in the pull request.
Only pull requests that have been tested and approved by GitHub Actions are eligible for being merged!
Note that GitHub Actions will only run the test suite for that particular repository. That is, for easyconfig contributions it does not include actually building and installing software.
For more information on the test suites, see Unit tests.
"},{"location":"contributing/#contributing_review_process_adding_tests","title":"Adding tests","text":"An implicit requirement for contributions, in particular contributions to the EasyBuild framework, is that they must be accompanied by additional tests or test cases.
For new features or enhancements, a dedicated test (case) must be added which verifies that the feature implementation works as expected.
For bug fixes, a test (case) must be added that triggers the code path where the bug manifested, and which verifies that the bug was indeed fixed.
Tests not only confirm that the implementation is correct, it also helps to ensure that any future changes will not break the functionality you contributed.
"},{"location":"contributing/#contributing_review_process_backward_compatibility","title":"Backward compatibility","text":"Contributions should retain backward compatibility, i.e., they should not make any changes that alter the (default) functionality of the existing code base. Of course, enhancements to existing code that retain backward compatibility can be made.
One exception to this rule is bug fixes, where the whole point is usually to fix functionality that was implemented incorrectly.
This also applies to existing easyconfig files; for example, the versions of dependencies should not be altered. Adding dependencies that were missing or otherwise enhancing existing easyconfigs (e.g., adding extra extensions, enabling additional features, etc.) are usually considered acceptable.
Changes that break backward compatibility have to be motivated well with technical arguments, and must be approved by the EasyBuild maintainers.
"},{"location":"contributing/#contributing_review_process_code_style","title":"Code style review","text":"Next to functional evaluation of contributions, care is also taken to maintain a consistent code style across the EasyBuild code base (see also Code style); contributions must take the (mostly PEP8) code style into account.
This aspect is sometimes considered to be needless overhead, yet it is an important aspect of the review process. A consistent code style is invaluable in a large code base that is constantly being updated by a worldwide community.
This also applies to easyconfig files, where we try to maintain a strict style that mostly matches the established PEP8 coding style for Python (since easyconfigs are written in Python syntax). However, also the grouping and ordering of easyconfig parameters is a part of the 'code' style we maintain.
An automated (partial) check to see whether easyconfig files are ready to be contributed can be performed via eb --check-contrib. This will check:
This check is also a part of the test suite run by GitHub Actions for easyconfig PRs.
"},{"location":"contributing/#contributing_review_process_review_pr","title":"Comparing with existing easyconfigs","text":"We try to maintain consistency across easyconfig files for a particular software package, across multiple software versions, toolchains and variants (with a different versionsuffix).
The easyconfig files to compare with are selected based on similarity, by combining two criteria, in order.
First, the software version is taken into account, using one of the following criteria:
The first combination of one of the software version criteria with one of the other criteria that yields one or more matching easyconfig files is used. If none of the combinations match, no easyconfig files for that particular software package are available yet, and no comparison is made.
For easyconfig contributions, one or more accompanying test reports must be submitted to confirm that the added and/or changed easyconfig files (still) work as expected.
We recommend that you submit a test report for your own easyconfig pull requests. Other people can also submit test reports to confirm that your contribution works as expected on their system(s).
With EasyBuild being properly configured (see GitHub: Configuration), this should be as simple as running eb --from-pr <PR#> --upload-test-report --force --robot.
See Uploading test reports for more information.
"},{"location":"contributing/#contributing_review_process_do_not_merge_your_own_prs","title":"Pull requests are merged by a maintainer other than the author","text":"A pull request should never be merged by its author.
This policy is maintained in order to ensure a \"two-pairs-of-eyes\" review process of all contributions.
"},{"location":"contributing/#contributing_review_process_why_pr_closed_by_maintainer","title":"Why a pull request may be closed by a maintainer","text":"Although it is generally avoided, there are a few reasons why maintainers might close a pull request:
This is done routinely as a way of focusing everyone's efforts on relevant contributions, and should not be seen as a rejection. In fact, contributors are encouraged to reopen the pull request if they feel it is still relevant.
"},{"location":"controlling-compiler-optimization-flags/","title":"Controlling compiler optimization flags","text":"This page provides an overview on the different ways in which compiler optimization flags used by EasyBuild can be controlled.
"},{"location":"controlling-compiler-optimization-flags/#controlling_compiler_optimization_flags_optarch","title":"Controlling target architecture specific optimizations via By default, EasyBuild optimizes builds for the CPU architecture of the build host, by instructing the compiler to generate instructions for the highest instruction set supported by the process architecture of the build host processor.
Optimizing for the processor architecture of the build host is usually what you want in an HPC cluster, but it has some implications if your cluster is heterogeneous (i.e., has different processor generations), or if you want to execute your applications in a machine with a processor architecture that is different from the one of the build host.
For example, if you compile your application optimized for an Intel Haswell processor (i.e. using AVX2 instructions), it will not run on a system with an older Intel Nehalem processor.
One possible workaround for heterogeneous HPC clusters is to build as many copies of the software stack as you have processor generations in your cluster, and to configure your system so each compute node uses the right software stack matching its processor architecture type. Details for one way of doing this, using automounter/autofs are available at https://easybuild.io/files/sciCORE-software-management_20150611.pdf.
Another solution is to configure EasyBuild to not optimize for the processor architecture of the build host via --optarch, see below.
"},{"location":"controlling-compiler-optimization-flags/#controlling_compiler_optimization_flags_optarch_caveats_hardcoding","title":"Build environment vs hardcoding in build scripts","text":"For example, the OpenBLAS build system will autodetect the processor architecture in the build host, and will optimize for that processor architecture by default.
If you want a generic OpenBLAS build you will need to tweak the OpenBLAS easyconfig file to define the desired TARGET to use. For this you will need to modify the buildopts easyconfig parameter, for example:
See these links for more details w.r.t. OpenBLAS:
When this is the case, EasyBuild will use the right compiler flags to optimize for a generic processor architecture, i.e. avoid using machine instructions that are only supported by very recent processors.
On other systems or for other compilers, you can check which compiler flags will be used via Extended dry run.
"},{"location":"controlling-compiler-optimization-flags/#controlling_compiler_optimization_flags_optarch_per_compiler","title":"Setting architecture flags for different compilers via Starting with version 3.1.0, EasyBuild supports specifying architecture flags on a per-compiler basis. This enables to \"set and forget\" the --optarch option for your compilers of interest, as opposed to change it depending on the compiler used on the packages to be installed.
The options for each compiler are set independently. That means that if a GCC-based toolchain is used, but the only compiler specified is Intel (for example with --optarch=Intel:xCORE-AVX2), then EasyBuild will behave as if --optarch was not specified for this toolchain.
As of EasyBuild v2.7.0, the support for using EasyBuild on Cray systems is considered stable. Tt enables building/installing software using the PrgEnv modules provided by Cray. This page provides an overview of the current status.
for providing us access to Cray systems, for their support and for testing and contributing to this work.
"},{"location":"cray-support/#test-systems","title":"Test systems","text":"An up-to-date list of software applications built on Cray systems at CSCS can be found https://github.com/eth-cscs/production/, see https://github.com/eth-cscs/production/tree/master/jenkins-builds.
"},{"location":"cray-support/#required-easybuild-configuration","title":"Required EasyBuild configuration","text":""},{"location":"cray-support/#modules-tool","title":"Modules tool","text":"You can also export this option as a shell variable. Example for sandybridge:
This file is loaded by default and contains enough information to build the easyconfig files shipped with EasyBuild.
Since EasyBuild v3.8.0, individual easyconfig files or particular (versions of) toolchains can be marked as deprecated.
"},{"location":"deprecated-easyconfigs/#deprecated_easyconfigs_symptoms","title":"Symptoms","text":"Using an easyconfig file or toolchain that was marked as deprecated results in a warning message like:
Or, in case you are trying to use an easyconfig file or toolchain that was marked deprecated in a previous major version of EasyBuild:
There are several possible reasons why a particular easyconfig file or toolchain was deprecated, some of which include:
Easyconfig files that are deprecated or which use a deprecated toolchain are not actively maintained, and are no longer included in the EasyBuild regression test (which means they may be broken by recent changes to the EasyBuild framework or relevant easyblocks).
In a future major version of EasyBuild, these easyconfig files will be archived (see also Archived easyconfigs).
"},{"location":"deprecated-easyconfigs/#deprecated_easyconfigs_toolchains","title":"Deprecated toolchains","text":"Some of the functionality that was available in previous EasyBuild versions is deprecated, and should no longer be used.
This functionality will be removed in a future version of EasyBuild (see Removed functionality for more information about functionality that has been removed already).
The different section below document the functionality that is deprecated in EasyBuild version, for which support will be removed in EasyBuild version 5.0.
Support for using Lmod 6.x as modules tool with EasyBuild has been deprecated, and will be removed in a future version of EasyBuild.
"},{"location":"deprecated-functionality/#depr_dummy_toolchain","title":"For more information, see System toolchain.
"},{"location":"deprecated-functionality/#deprecation_policy","title":"Deprecation policy","text":"With every EasyBuild release, we try very hard to maintain backward compatibility. That is, EasyBuild version X.Y should still build software packages that could be built with EasyBuild version X.(Y-1), without requiring modifications to the used easyconfig file or easyblock.
However, every now and then a breaking change needs to be made to EasyBuild, because of design decisions or to resolve mistakes that were made in the past. These changes involve deprecating the behaviour or functionality we want to get rid of, together with supporting a better alternative.
You can (temporarily) still rely on the deprecated functionality by specifying a lower version via --deprecated to overrule that setting, until the functionality is actually disabled.
"},{"location":"detecting-loaded-modules/","title":"Detection of loaded modules","text":"Running EasyBuild in an environment where one or more (EasyBuild-generated) modules are loaded may interfere with the software installations performed by EasyBuild, i.e.:
Since manually loading modules may affect the reproducibility of software installations, it should be discouraged.
In EasyBuild versions before v3.3.0, having a loaded module for the same software packages as the one being installed resulted in an EasyBuild error message.
Since EasyBuild v3.3.0 a more extensive detection mechanism is available and the action that should be taken for loaded modules can be controlled via --detect-loaded-modules. Having a module loaded for any software package that is being installed still results in a hard error.
"},{"location":"detecting-loaded-modules/#detecting_loaded_modules_mechanism","title":"Detection mechanism","text":"Detecting loaded EasyBuild-generated modules is done by checking the environment for defined $EBROOT* environment variables. If any are found, the corresponding loaded module is determined for better reporting.
The action that should be taken when one or more loaded (EasyBuild-generated) modules are detected can be specified via the --detect-loaded-modules configuration option.
The specified action is only taken for non-allowed loaded modules, see Allowing particular loaded modules.
"},{"location":"detecting-loaded-modules/#detecting_loaded_modules_action_error","title":"This is equivalent to the behaviour of EasyBuild versions prior to version 3.3.0.
The warning is intended to make the user aware that the environment in which EasyBuild is being run is not clean.
This is the default behaviour in EasyBuild v3.3.0 and newer.
"},{"location":"detecting-loaded-modules/#detecting_loaded_modules_allow","title":"Allowing particular loaded modules","text":"By default, only EasyBuild itself is considered as an allowed module.
Hence, EasyBuild will detect this and act on it, according to the value specified to --check-ebroot-env-vars:
This is the default behaviour in EasyBuild v3.3.0 and newer.
"},{"location":"easyconfig-files-local-variables/","title":"Local variables in easyconfig files","text":"This page discusses the use of local variables in easyconfig files.
For more general information on writing easyconfig files, please see Writing easyconfig files: the basics.
"},{"location":"easyconfig-files-local-variables/#easyconfig_files_local_variables_motivation","title":"Motivation & context","text":"When composing easyconfig files, it can sometimes make sense to use one or more local variables to define easyconfig parameters in a cleaner way, for example to avoid copy-pasting values that are used multiple times, or to avoid too long lines (longer than the maximum width of 120 characters as specified in Code style). A local variable within the context of easyconfig files is any variable that does not correspond to a known easyconfig parameter (either general of easyblock-specific).
One thing that is easily overlooked is the importance of how these local variables are named: you should try and avoid that the names of local variables will match with the name of an easyconfig parameter that may get introduced in future EasyBuild versions. If that would happen, the semantics of the easyconfig file will change which may either result in a broken installation or perhaps a different installation than was intended (which could be worse than a broken one).
Avoiding that names of local variables are close to the name of (future) easyconfig parameters is also important, because of the \"typo detection\" feature that EasyBuild has: if the name of a local variable is too close to a known easyconfig parameter, EasyBuild will assume you have made a mistake, and will report a typo error, for example:
Some changes were made in EasyBuild v4.0 to discourage the use of poorly named local variables:
To ensure that local variables used in easyconfig files do not clash with easyconfig parameters that get added in future EasyBuild versions, we have defined a recommended naming scheme for local variables.
A check was added in EasyBuild v4.0 to ensure that the names of known easyconfig parameters do not conform to any of these rules, to ensure that local variables can always be discriminated from known easyconfig parameters.
"},{"location":"easyconfig-files-local-variables/#easyconfig_files_local_variables_naming_warning","title":"Warning for local variables that do not follow the recommended naming scheme","text":"By default, EasyBuild will produce a clear warning when one or more local variables are used that do not conform to the Recommended naming scheme for local variables in easyconfig files.
The default is set such that non-confirming local variables are only reported through a printed warning, but do not result in cancelling the installation (since they're usually not actually problematic).
"},{"location":"easyconfig-files-local-variables/#easyconfig_files_local_variables_fix_deprecated_easyconfigs","title":"Renaming local variables to match the recommended naming scheme using To fix one or more easyconfig files that includes local variables that do not follow the Recommended naming scheme for local variables in easyconfig files, eb --fix-deprecated-easyconfigs can be used.
There are a couple of caveats here though...
This means that it may make some unintended changes, so make sure to always double check which changes were made!
In addition, it sometimes make more sense to simply eliminate the local variable rather than renaming it, for example when it wasn't really needed at all: maybe it was only actually used once, or maybe using a template like %(pyver)s or (pyshortver)s (see also Available template values for easyconfigs) renders it obsolete.
"},{"location":"easyconfigs-search-index/","title":"Using an index to speed up searching for easyconfigs","text":"EasyBuild often needs to search for Easyconfig files (or accompanying files like patches), either based on command line arguments (like the name of an easyconfig file) or options to the eb command (like --search, see Searching for easyconfigs), or to resolve dependencies for a particular easyconfig file that was parsed already.
Searching for easyconfig files or patches may take a while, since it can potentially involve weeding through thousands of files, which may be located on a shared filesystem (where metadata-intensive operations like file searching can be rather slow).
If EasyBuild turns out to be sluggish when searching for easyconfig files in your setup, using an index file could make a big difference.
Support for index files was implemented in EasyBuild version 4.2.0 .
"},{"location":"easyconfigs-search-index/#easyconfigs_index_create","title":"Creating an index","text":"Make sure to create an index for the correct path.
The search for easyconfig files performed by EasyBuild will not recurse into subdirectories of the locations it considers (see Searching for easyconfigs: the robot search path), other than those with a name matching the software for which it is trying to find an easyconfig file (like t/TensorFlow/ when searching for an easyconfig file for TensorFlow).
EasyBuild will automatically pick up and use any index file that it runs into while searching for easyconfig files or patches. If an index file is found, it will be preferred over walking through the directory tree to check for the target file, which is likely to significantly speed up the search operation.
When a (valid) index file is found for a particular path, a message will be printed mentioning \"found valid index for...\":
One potential issue with having an index in place is that it may get outdated: new files may have been added to the directory since the index was created or last updated.
If updating the indexes is not an option (see Updating an existing index), you can instruct EasyBuild to ignore any existing indices using the --ignore-index configuration option.
The only downside of this option is that searching for easyconfig files may be significantly slower. Any existing index files are left untouched (they will not be updated or removed).
"},{"location":"easyconfigs-search-index/#easyconfigs_index_max_age","title":"Controlling how long the index is valid","text":"When creating an index file, you can specify how long the index should be considered valid.
Trust us here, December 31st 9999 is the end of times. Better get prepared.
"},{"location":"easyconfigs-search-index/#easyconfigs_index_release","title":"Index included with EasyBuild releases","text":"Each EasyBuild release (since EasyBuild v4.2.0) comes with an index file for the easyconfig (and patch) files that are included with that release.
Whether or not you should create an index file for your directories housing additional easyconfig files depends on a number of factors, including:
Keep in mind that creating an index implies also updating it frequently, to ensure that EasyBuild will take all available files in account.
"},{"location":"easystack-files/","title":"Easystack files","text":"This documentation covers aspects of specifying a software stack to install with Easybuild with easystack files.
Note: this is an experimental feature. Some of the mentioned functionality may be subject to change or be prone to errors.
Some breaking changes were made to the experimental easystack support in EasyBuild v4.7.0.
Easystack files describe an entire software stack, and can be used to specify to EasyBuild what to install.
"},{"location":"easystack-files/#easystack_usage","title":"Usage","text":"Easystack files are written in YAML syntax.
Essentially, an easystack file lists the easyconfig files you want to install, which are specified under the easyconfigs key.
You need to take care with some values in YAML, especially integers, booleans, etc.
If the specified value definitely must be a string value, you should use quotes ('...') to avoid that the YAML parser automatically converts the value to be of a specific type.
This is not recommended however, as short options are more difficult to interpret by humans.
When building software with an easystack file, you can still add additional options on the command line as well. These apply to all items in the easystack file. For example, if you have an easystack file named my_easystack.yaml
Note that options specified on the command line are placed before the easyconfig-specific options in the easystack file. EasyBuild will always respect the argument that was put last.
Since easyconfig-specific configuration options specified in the easystack file are put last, they take priority over the the ones on the command line, if the same configuration option is specified in both.
In the future, we are planning to support additional also global options specified in the easystack file. For example:
Additionally, we plan to support specifying for which EasyBuild version an easystack file was intended, which can be helpful in more accurately recreating a certain software stack (see issue #4106).
Finally, we plan to support specifying labels, which would make it more easy to install only a certain subset of the items listed in an easystack file. For example, by labelling all GPU-capable software with a gpu label, one could easily choose to not build anything labeled gpu on a CPU node (see issue #3512).
"},{"location":"experimental-features/","title":"Experimental features","text":"First introduced in EasyBuild v2.1.0 (see EasyBuild v2.1.0 Release Notes), experimental features can only be used by enabling the --experimental configuration option.
An experimental feature indicates to users that these features may change significantly in a future release and should be used only for testing, not (yet) for production usage.
All time-consuming operations, including executing commands to configure/build/install the software, are only reported rather than being actually performed.
Example output is available at Extended dry run: examples.
"},{"location":"extended-dry-run/#extended_dry_run_notes","title":"Important notes","text":"The actual build and install procedure may (slightly) differ from the one reported by --extended-dry-run, due to conditional checks in the easyblock being used.
For example, expressions that are conditional on the presence of certain files or directories in the build directory will always be false, since the build directory is never actually populated.
"},{"location":"extended-dry-run/#extended_dry_run_notes_ignored_errors","title":"Errors are ignored (by default) during dry run","text":"Any errors that occur are ignored, and are reported with a clear warning message. This is done because it is possible that these errors occur because of the dry run mechanism.
For example, the install step could assume that certain files created by a previous step will be present, but they will not be there since the commands that are supposed to produce them were not actually performed in dry run mode.
Errors are ignored on a per-step basis. When an error is ignored in a particular step, that step is aborted, which may result in partial dry run output for that particular step. Subsequent steps will still be run (in dry run mode), however.
Since it's possible that these errors occur due to a bug in the easyblock being used, it's important to pay attention to these ignored errors.
At the end of dry run output, another warning message is shown if any ignored errors occurred:
Ignoring errors that occur during a dry run is enabled by default; it can be disabled using the configuration option that is available for it, i.e. by:
During an extended dry run, several operations are not performed, or are only simulated.
The sections below give a detailed overview of the dry run mechanism.
"},{"location":"extended-dry-run/#extended_dry_run_overview_build_install_dirs","title":"Temporary directories as build/install directories","text":"To make very sure that EasyBuild does not touch any files or directories during the dry run, the build and (software/module) install directories are replaced by subdirectories of the temporary directory used by that particular EasyBuild session.
Although the build and install directories are effectively temporary directories during a dry run (under a prefix like /tmp/eb-aD_yNu/__ROOT__), this is not visible in the dry run output: the 'fake' build and install directories are replaced by the corresponding original value in the dry run output. For example:
The build (sub)directory used during an actual (non-dry run) EasyBuild session may be different than the one mentioned in the dry run output.
This is because during a dry run, EasyBuild will guess the name of the subdirectory that is created by unpacking the first source file in the build directory as being <name>-<version>. Although this is a common pattern, it is not always 100% correct.
For example, you may see this in the dry run output for WRF (for which a build-in-installdir procedure is used):
The actual build (and install) subdirectory is slightly different while not in dry run mode however, i.e.: /home/example/eb/software/WRF/3.6.1-intel-2015a-dmpar/WRFV3.
"},{"location":"extended-dry-run/#extended_dry_run_overview_downloading","title":"No downloading of missing source files/patches","text":"Required files (source files/patches) are not downloaded during a dry run if they are not available yet.
The dry run output will specify whether files are found (and if so, at which path) or not; the exact output for files that were not found depends on whether or not source URLs are available.
If the source file is already available in the source path that EasyBuild was configured with, it is indicated as such:
In case no source URLs are available and required files are missing, they are simply marked as such:
However, since the dry run mechanism never actually uses the source files/patches, this does not affect the remainder of the output of --extended-dry-run/-x.
"},{"location":"extended-dry-run/#extended_dry_run_overview_checksum_verification","title":"Checksum verification is skipped","text":"Computing checksums of sources files/patches, and verifying them against specified checksums (if available) is skipped during a dry run, because it is considered potentially too time-consuming. In addition, source files/patches may not be available anyway.
Source files are not unpacked, since this may require too much time (in case of large source files). Additionally, source files may not be available anyway.
Since source files are not unpacked, patch files can not applied either.
The dry run output does provide an overview of patch files, together with where they are found and how they are applied:
Likewise, runtime patching performed by the easyblock itself can not work either. If the apply_regex_substitutions function (available from easybuild.tools.filetools) is used, a clear overview is included in the dry run output (see also Runtime patching of files).
The dry run output includes an overview of the modules being loaded. In addition an overview of all loaded modules, including the ones that were loaded indirectly, is shown.
Only modules that were effectively loaded will appear in the full list of modules being printed; modules for which the load was simulated will not be included.
"},{"location":"extended-dry-run/#extended_dry_run_overview_module_load_simulated_deps","title":"Simulated loading of non-available dependency modules","text":"For example, for netCDF used as a dependency for WRF the following is included in the module file contents included in the dry run output:
When the module that corresponds to the toolchain being used is not available, the dry run mechanism will also simulate the module load statements for the individual toolchain components, to ensure that version checks on the toolchain components can work as expected.
The build environment that is set up based on the toolchain (and toolchain options) being used, and the dependencies being loaded is reported as a part of the dry run output.
This is particularly useful as an overview of which environment variables that are defined by the toolchain mechanism, and to assess the effect of changing toolchain options.
The output is deliberately formatted such that is can be easily copy-pasted, which can be useful to mimic the environment in which EasyBuild will perform the build and install procedure.
"},{"location":"extended-dry-run/#extended_dry_run_overview_run_cmd","title":"Shell commands are not executed","text":"This typically includes the commands that are defined in the easyblock to be run as a part of the configure/build/install steps.
There are a couple of minor exceptions though. Some (light-weight) commands are always run by the EasyBuild framework, even in dry run mode, and an easyblock can specify that particular commands must always be run (see also Executing commands).
"},{"location":"extended-dry-run/#extended_dry_run_overview_sanity_check","title":"Sanity check paths/commands are not checked","text":"Since nothing is actually being installed during a dry run, the sanity check paths/commands can not be checked.
Instead, the dry run mechanism will produce a clear overview of which paths are expected to be found in the installation directory, and which commands are expected to work (if any).
During a dry run, the contents of the module file that would be installed is still generated, but only printed; it is not actually written to file.
More importantly however, the module file being reported is bound to be incomplete, since the module generator only includes certain statements conditionally, for example only if the files/directories to which they relate actually exist. This typically affects prepend-path statements, e.g. for $PATH, $LD_LIBRARY_PATH, etc.
Although errors are just ignored by the dry run mechanism on a per-step basis, they may hide subsequent operations and useful information for the remainder of the step (see also Errors are ignored (by default) during dry run).
"},{"location":"extended-dry-run/#extended_dry_run_guidelines_easyblocks_detect_dry_run","title":"Detecting dry run mode and enhancing the dry run output","text":"To detect whether an easyblock is being used in dry run mode, it suffices to check the self.dry_run class variable.
Rather than assuming that particular files or directories will be there, easyblocks should take into that they may not be, for example because EasyBuild is being run in dry run mode.
Easyblocks that do not take this into account are likely to result in ignored errors during a dry run (see also Errors are ignored (by default) during dry run). For example, for the bad example shown above:
The EasyBuild framework provides a bunch of functions that are \"dry run-aware\", and which can significantly help in keeping easyblocks free from conditional statements checking self.dry_run:
When triggered in dry run mode, this will result in a clear dry run message like:
This is used in a couple of places in the EasyBuild framework, to avoid some environment variables being defined cluttering the dry run output without added value. It can be used for similar reasons in easyblocks.
To make runtime patching of files in easyblocks easier, and to do it with taking the possibility of being in dry run module into account, the EasyBuild framework provides the apply_regex_substitutions function (available from the easybuild.tools.filetools module, since EasyBuild v2.4.0).
This function takes two arguments: a path to the file that should be patched, and a list of tuples specifying the regular expression pattern to match on, and the string value that should be used as replacement text.
In their simplest form, they simply take the command to execute as a string. For example:
In dry run mode, these functions just produce a dry run message, rather than actually executing the specified command. For example:
Take into account that the directory included in the message may not be 100% accurate, see Note on build directory in dry run mode.
"},{"location":"extended-dry-run/#silently-executing-commands","title":"Silently executing commands","text":"Sometimes, it can be required that specific (light-weight) commands are always executed, because they have side-effects that are assumed to have taken place later in the easyblock.
This is mainly intended for use in the EasyBuild framework itself, where commands that verify certain things must be executed, but it can also be useful for easyblocks (if used correctly).
The following diagram shows the main steps carried out by EasyBuild for a regular software installation with the eb command:
The scope of the EasyBuild execution is ultimately defined by the target easyconfig files given in the eb command. They will define the number of actions to carry out, such as software installations, fetching of sources or opening of PRs. Therefore, target easyconfig files are parsed early in the process, just after the runtime options have been resolved. The tooling to parse easyconfig files is located in a specific tools module in easybuild.framework.easyconfig.tools, while the EasyConfig class is found in easybuild.framework.easyconfig.easyconfig.
Once the easyconfig files are properly parsed, a common action is to resolve the dependencies for those installations with the --robot option. This is handled in easybuild.tools.robot which provides methods to search easyconfig files, resolve dependencies, and check conflicts between software packages.
The installation procedure of each software package is defined by the easyblock attached to it. This means that EasyBuild creates an EasyBlock instance for each individual installation and determines the easyblock to use from the easyconfig file. Once the EasyBlock instance is created, EasyBuild will call its run_all_steps() method to execute the installation steps defined for that software.
"},{"location":"framework-overview/#step_wise_install","title":"Step-wise Installation Procedure","text":"Most of the steps in the initial Arrangement phase are already covered to some extent in the EasyBlock class, such as:
Once the target easyconfig file is read and all its parameters are validated, they will be accessible through different attributes and methods of the EasyConfig object. The main examples are:
The EasyConfig instance is also accessible from the corresponding EasyBlock instance through its EasyBlock.cfg attribute.
"},{"location":"framework-overview/#easystack-class","title":"EasyStack class","text":"EasyStacks are an experimental feature in active development.
A toolchain in EasyBuild is much more than just a bundle of libraries and compilers to build and run software in a consistent environment. Toolchains are defined by their own classes built on top of the Toolchain class.
Toolchains are modular. Each toolchain component (i.e compiler, numerical library, MPI implementation) is defined by its own child class or by multiple ones. These components are combined in sub-toolchains (e.g. the gompi toolchain) which can then be re-combined with other components in bigger toolchains (e.g. the foss toolchain). Therefore, the resulting options of the toolchain, its attributes and methods will be the combined result of all inherited class components.
Check the Configuring EasyBuild for details on how to use the different configuration mechanisms.
In the case of EasyBuild, the main complication to report issues and bugs might be to determine if the issue/bug at hand does actually originate in easybuild-framework or if instead it belongs in easybuild-easyblocks or easybuild-easyconfigs. It is not uncommon that the traceback of bugs in easyblocks or easyconfigs reach the codebase in easybuild.framework or easybuild.tools.
Nevertheless, do not worry too much if you cannot determine which repository to target with your issue/bug. In case of doubt, easybuild-framework is the best bet in general and maintainers can move issues between EasyBuild repositories if needed.
"},{"location":"framework-overview/#pull-requests","title":"Pull requests","text":"Since v3.5.0, EasyBuild supports hooks that can be used to customise the behaviour of EasyBuild according to site policies if needed, without having to change the EasyBuild framework or the existing easyblocks.
"},{"location":"hooks/#what-are-hooks","title":"What are hooks?","text":"Hooks are user-defined functions that are called by the EasyBuild framework at specific times during the installation procedure. They can be leveraged to alter or augment the installation procedure.
This is usually done to conform with site-specific policies that are difficult to enforce otherwise, but it can also be (ab)used to fix specific problems or inject self-implemented enhancements (before you flesh them out in a proper contribution, for example).
To instruct EasyBuild to use your hook implementations, you only need to specify the location of the Python module (*.py) that implements them.
The list of currently available hooks in order of execution, which can also be consulted using eb --avail-hooks, is:
All functions implemented in the provided Python module for which the name ends with _hook are considered.
In hooks you have access to the full functionality provided by the EasyBuild framework, so do import from easybuild.tools.* (or other easybuild.* namespaces) to leverage those functions.
It is recommended to anticipate possible changes in the provided (named) arguments, using the *args and **kwargs mechanism commonly used in Python. This avoids that your hook implementations may break when updating to future EasyBuild versions. For example:
The return value of a hook is usually ignored by EasyBuild, except in particular cases:
This is important since it allows to dynamically modify easyconfig files while they are still \"raw\", i.e. when the easyconfig parameter values are still basic Python data structures like lists, dictionaries, etc. that are easy to manipulate (see also Manipulating easyconfig parameters).
Due to internal details of the EasyBuild framework, you may run into some surprises when implementing hooks. Here are some things to take into account:
"},{"location":"hooks/#resolving-of-template-values","title":"Resolving of template values","text":"In all step hooks, template values in easyconfig parameters will be resolved whenever they are accessed.
There is one notable exception to this: Templates in easyconfig parameters are not resolved in parse_hook, because templating has been disabled explicitly before parse_hook is called; this helps significantly to simplify manipulating of easyconfig parameter values (see also Manipulating easyconfig parameters).
"},{"location":"hooks/#manipulating-easyconfig-parameters","title":"Manipulating easyconfig parameters","text":"You may run into surprises when trying to manipulate easyconfig parameters, for various reasons.
First of all, the original easyconfig parameters may already be processed in another data structure which does not resemble the original format in which the parameter was defined in the easyconfig file.
Moreover, this processing could be done either \"in place\" by replacing the original easyconfig parameter value, or in a separate variable, which effectively means that any changes to the original easyconfig parameter value are simply ignored.
In addition, because of how the templating mechanism for easyconfig parameter works, changes to easyconfig parameters with non-string values (i.e. lists, dictionaries, etc.) will go up in smoke if not done correctly.
More specifically, the following approach will not work in any of the (step) hooks, except for parse_hook:
EasyBuild archives the easyconfig file that was used for a particular installation: A copy is stored both in the easybuild subdirectory of the software installation directory and in the easyconfigs repository (see Easyconfigs repository).
If any changes were made to the easyconfig file via hooks, these changes will not be reflected in these copies. The assumption here is that the hooks will also be in place for future (re-)installations.
EasyBuild does however store an additional copy of the easyconfig file which includes any modifications that were done dynamically, for example by hooks. If subtoolchains were used to resolve dependencies, they will also be hardwired in this copy.
If an unknown hook is used then EasyBuild will error (see Available hooks). The following example only adds the pre_build_and_install_loop_hook if the EasyBuild version is >= \"4.8.1\".
This documentation covers aspects of implementing easyblocks and how to use them. For a concise definition of easyblocks, see Easyblocks.
"},{"location":"implementing-easyblocks/#implementing_easyblocks_basics","title":"The basics","text":"An easyblock is a Python module that implements a software build and installation procedure.
This concept is essentially implemented as a Python script that plugs into the EasyBuild framework.
EasyBuild will leverage easyblocks as needed, depending on which software packages it needs to install. Which easyblock is required is determined by the easyblock easyconfig parameter, if it is present, or the software name (see Generic vs software-specific easyblocks).
"},{"location":"implementing-easyblocks/#implementing_easyblocks_generic_vs_software_specific","title":"Generic vs software-specific easyblocks","text":"Easyblocks can either be generic or software-specific.
Generic easyblocks implement a 'standard' software build and installation procedure that is used by multiple different software packages. A commonly used example is the ConfigureMake generic easyblock, which implements the standard configure - make - make install installation procedure used by most GNU software packages.
Software-specific easyblocks implement the build and installation procedure for a particular software package (see also Module name/location). Typically this involves highly customised substeps, for example specifying dedicated configuration options, creating or adjusting specific files, executing non-standard shell commands, etc. Usually a custom implementation of the sanity check is also included.
The distinction between generic and software-specific easyblocks can be made based on the naming scheme that is used for an easyblock (see also Naming scheme for easyblocks).
See also .
"},{"location":"implementing-easyblocks/#implementing_easyblocks_vs_easyconfigs","title":"Easyblocks vs easyconfigs","text":"Before you start implementing an easyblock, you should determine whether or not you really need an easyblock.
Easyconfig files provide quite a bit of flexibility that alleviate the need for implementing many (software-specific) easyblocks. Examples include easyconfig parameters like (pre){config,build,installopts} (available for any easyblock), install_cmd (only for Binary generic easyblock or derivates), etc. See Writing easyconfig files: the basics for an overview of what is supported in easyconfig files, and for custom easyconfig parameters for the existing generic easyblocks (see also 'eb -e <easyblock> -a').
On the other hand, somewhat complex or heavily customised software build and installation procedures may be handled better via a custom easyblock.
Easyblocks are \"do once and forget\", and can provide a central solution for peculiarities of installations. Since they are basically Python scripts, they are very flexible and can take care of the 'heavy lifting' that goes beyond the key-value defining scope of easyconfig files.
Hence, there is a fine line between using 'fat' easyconfigs with a generic easyblock and using a custom software-specific easyblock.
One important aspect to consider of course is that implementing easyblocks requires some familiarity with Python, while easyconfig files can mostly be seen as a set of pure key-value definitions and hence are easier to create or update.
"},{"location":"implementing-easyblocks/#implementing_easyblocks_naming_scheme","title":"Naming scheme for easyblocks","text":"Easyblocks need to follow a strict naming scheme, to ensure that EasyBuild can pick them up as needed. This involves two aspects: i) the name of the Python class, and ii) the name and location of the Python module file.
"},{"location":"implementing-easyblocks/#implementing_easyblocks_naming_scheme_class_name_specific","title":"Class name for software-specific easyblocks","text":"The name of the Python class is determined by the software name for software-specific easyblocks. It consists of a prefix 'EB_', followed by the (original) software name.
Because of limitations in Python on characters allowed in names of Python classes, only alphanumeric characters and _ are allowed. Any other characters are replaced following an encoding scheme:
For code style reasons, the class name should start with a capital letter.
The name of the Python module file is directly related to the name of Python class (i.e., the actual easyblock) that it provides.
The location of the Python module is determined by whether the easyblock is generic or software-specific. Generic easyblocks are located in the easybuid.easyblocks.generic namespace, while software-specific easyblocks live in the easybuild.easyblocks namespace directly. To keep things organised, the actual Python module file for software-specific easyblocks are kept in 'letter' subdirectories, rather than in one large 'easyblocks' directory (see https://github.com/easybuilders/easybuild-easyblocks/blob/main/easybuild/easyblocks/).
Note that you shouldn't concern yourself too much with getting the location of an easyblock right, as long as you use --include-easyblocks to make EasyBuild use additional or customised easyblocks (see Including additional easyblocks (--include-easyblocks) for more information).
"},{"location":"implementing-easyblocks/#implementing_easyblocks_structure","title":"Structure of an easyblock","text":"Typically some useful functions provided by the EasyBuild framework are imported at the top of the Python module.
When implementing an easyblock, it is common to derive from an existing (usually generic) easyblock, and to leverage the functionality provided by it. This approach is typically used when only a specific part of the build and installation procedure needs to be customised.
All of the parameters which are \"set\" in an easyconfig file (see Available easyconfig parameters) become key-value pairs in the self.cfg dictionary. For instance, if the easyconfig file specifies
You can use this notation successfully in your easyblock. A few of the most commonly used parameters can be referenced directly,
The other easyconfig parameters, and any additional custom parameters which you define for your own easyblock, will not be automatically mapped. You will need to use self.cfg to access them in your code.
"},{"location":"implementing-easyblocks/#implementing_easyblocks_custom_parameters","title":"Custom easyconfig parameters","text":"In an easyblock, additional custom easyconfig parameters can be defined to steer the behaviour of the easyblock. This is done via the extra_options static method. Custom parameters can be defined to be mandatory or optional.
The first element in the list of a defined custom parameter corresponds to the default value for that parameter (both None in the example above). The second element provides some informative help text, and the last element indicates whether the parameter is mandatory (MANDATORY) or just a custom parameter (CUSTOM).
"},{"location":"implementing-easyblocks/#implementing_easyblocks_constructor","title":"Easyblock constructor","text":"File manipulation is a common use case for implementing easyblocks, hence the EasyBuild framework provides a number of useful functions related to this, including:
This makes sure that the changes being made to the specified environment variable are kept track of, and that they are handled correctly under --extended-dry-run.
"},{"location":"implementing-easyblocks/#implementing_easyblocks_logging","title":"Log statements","text":"For software-specific easyblocks, a custom sanity check is usually included to verify that the installation was successful or not.
You can both specify file path and subdirectories to check for, which are specified relative to the installation directory, as well as simple commands that should execute successfully after completing the installation and loading the generated module file.
Note that it is up to you how extensive you make the sanity check, but it is recommended to make the check as complete as possible to catch any potential build or installation problems that may occur.
"},{"location":"implementing-easyblocks/#implementing_easyblocks_version_specific","title":"Version-specific parts","text":"In some case, version-specific actions or checks need to be included in an easyblock. For this, it is recommended to use LooseVersion rather than directly comparing version numbers using string values.
Some special care must be taken to ensure that an easyblock is fully compatible with --extended-dry-run / -x (see Extended dry run) and --module-only (see Only (re)generating (additional) module files using --module-only).
Before testing your easyblock implementation by actually building and installing the software package(s) it was implemented for, it is recommended to:
EasyBuild's capabilities can be extended easily, by including additional Python modules that implement support for building and installing software that is not supported (yet), define additional module naming schemes, or introduce additional toolchains, (optionally) with support for additional compilers, MPI libraries, linear algebra libraries, etc.
Since EasyBuild v2.2.0, dedicated configuration options are available that make it straightforward to get EasyBuild to pick up additional Python modules, and get them registered in the appropriate easybuild subnamespace.
These paths can be absolute or relative paths, or so-called glob patterns, i.e., paths containing wildcard characters like * or ?. The latter can be used to include several Python modules at once.
Examples of correct path specifications containing wildcards: - in a configuration file (no escaping of wildcards required): include-easyblocks = /home/example/myeb/*.py - using an environment variable: export EASYBUILD_INCLUDE_EASYBLOCKS=\"$HOME/myeb\\*.py\" - on the command line: eb --include-easyblocks='/home/example/myeb/*.py' ....
"},{"location":"including-additional-python-modules/#how-it-works","title":"How it works","text":"It is recommended to only override existing components during testing. Future EasyBuild versions may include important updates like bug fixes, which may be missed if customised implementations of components were put in place.
"},{"location":"including-additional-python-modules/#include_easyblocks","title":"Including additional easyblocks","text":"Adding support for building and installing additional software packages can be done by specifying the location of Python modules that implement easyblocks via --include-easyblocks.
Since EasyBuild 4.2.0, easyblocks from a pull request on GitHub can also be included, using --include-easyblocks-from-pr (see Using easyblocks from pull requests).
"},{"location":"including-additional-python-modules/#example","title":"Example","text":"The example below shows how all self-implemented easyblocks (both software-specific and generic) located in the $HOME/myeasyblocks directory can be included:
To make EasyBuild aware of one or more custom module naming schemes, the path to the corresponding Python modules can be specified via --include-module-naming-schemes.
Plugging in Python modules that add support for additional toolchains, optionally including additional toolchain components (compilers, MPI libraries, BLAS/LAPACK/FFT libraries, ...) can be done via --include-toolchains.
EasyBuild will determine whether the Python module is a toolchain definition or implements support for an additional toolchain component based on the name of the directory in which it is located. Implementations of toolchain components are expected to be located in a directory named according to the type of component (compiler, mpi, linalg or fft).
The example below shows how the support for additional toolchains and the required additional compiler/MPI toolchain components implemented by the Python modules located in the directory $HOME/myebtcs can be included:
Do take into account the list of (required) dependencies (see Dependencies).
"},{"location":"installation-alternative/#standard-installation-of-latest-release","title":"Standard installation of latest release","text":"Usually, you just want to install the latest (stable) version of each of the EasyBuild packages (framework, easyblocks, easyconfigs).
Python provides a couple of ways to do that. Every version of the EasyBuild packages is released via PyPi.
"},{"location":"installation-alternative/#alt_inst_easy_install_pip","title":"Installing EasyBuild without admin rights","text":"If you do not have EasyBuild installed yet, or if you just want to install the most recent version of each of the EasyBuild packages, you can use one of the following simple commands:
If you do have admin rights on the system where you want to install EasyBuild, you can simply omit the --prefix $HOME/EasyBuild/ to have EasyBuild installed system-wide. In that case, you do not need to touch the $PATH or $PYTHONPATH environment variables since the eb command will be installed in one of the default paths.
"},{"location":"installation-alternative/#alternatives-to-prefix","title":"Alternatives to To install one of the EasyBuild packages from a downloaded source tarball, use the following steps:
Do note that when an EasyBuild package is being installed without having the EasyBuild packages that it depends upon available, both easy_install and pip will try and pull in the latest available version of those packages from PyPi.
Thus, to have full control over the EasyBuild installation, you need to respect the following installation order: easybuild-framework, easybuild-easyblocks, easybuild-easyconfigs. The easyblocks package depends on the framework package; the easyconfigs package depends on both the framework and easyblocks packages.
To install the latest (stable) release of an EasyBuild package directly from GitHub, use the following command:
Again, the order in which the EasyBuild packages are installed is important to have full control over the installation process, see previous section.
"},{"location":"installation-alternative/#installation-of-latest-development-version","title":"Installation of latest development version","text":"To install the latest development version of an EasyBuild package from GitHub, you can simply adjust the command from the previous section to install from the develop branch (or any of the available feature branches in any EasyBuild repository for that matter):
You should use this only if you are interested in developing for EasyBuild. Although it is well tested, the development version of the EasyBuild repositories may be unstable at a given point in time.
"},{"location":"installation-alternative/#install_latest_develop_using_script","title":"Installation of latest development version using provided script","text":"After you have forked each of the EasyBuild repositories on GitHub (+ vsc-base), you can set up a development version of EasyBuild using the install-EasyBuild-develop.sh script.
The above creates a module file which you can load/inspect at will.
The interesting aspect about it is that it is pointing to an EasyBuild installation directly on local git repositories, which allows you to customise it easily. Remember to commit/push or otherwise save your changes, if you intend to use them later.
"},{"location":"installation/","title":"Installing EasyBuild","text":"EasyBuild is Python software, so there are a couple of ways to install it.
It is also possible to install EasyBuild as a module. To do this, use the 3-step procedure outlined at Installing EasyBuild with EasyBuild.
Do take into account the required and optional dependencies (see Requirements and Dependencies).
Notes on other ways of installing EasyBuild are available under section Alternative installation methods.
"},{"location":"installation/#requirements","title":"Requirements","text":"For more information on dependencies, see Dependencies.
"},{"location":"installation/#pip","title":"Using pip to Install EasyBuild","text":"Since EasyBuild is released as a Python package on PyPI you can install it using pip, the most commonly used tool for installing Python packages.
You may need to tweak this command a bit, depending on your setup, see Additional pip install options.
There are various other ways of installing Python packages, which we won't cover here. If you are familiar with other tools like virtualenv or pipenv, feel free to use those instead to install EasyBuild.
"},{"location":"installation/#sanity-check","title":"Sanity check","text":"The Tcl/C Environment Modules (version <= 3.2.10) does its default sorting differently than newer versions of Environment Modules and Lmod. The former will normally sort in the lexicographic order, while the latters follow an approach that is closer to Python's construct LooseVersion way of ordering. Such aspects may make a big difference, if you have installed both versions 1.9.0 and 1.15.2, with respect to what is the version being loaded by default.
On systems where both Python 2 and Python 3 are installed you may also have different pip commands available. Or maybe pip is not available at all, and only \"versioned\" pip commands like pip3 are available.
Keep in mind that you will have to make these environment changes again if you start a new shell session. To avoid this, you can update one of the shell startup scripts in your home directory (.bashrc for example).
"},{"location":"installation/#more_pip_env_PATH","title":"Updating This is not required if you installing EasyBuild in a standard system location.
If you want to control which Python version is used to run EasyBuild, you can specify the name or the full path to the python command that should be used by the eb command via the $EB_PYTHON environment variable.
If you prefer having EasyBuild available through an environment module file, you can consider installing EasyBuild with EasyBuild. This can be done in 3 steps:
If you don't have EasyBuild installed yet, you need to install it in a temporary location first. The recommended way of doing this is using pip to install EasyBuild.
Once you have a working (recent) temporary EasyBuild installation, you can use it to install EasyBuild as a module. Usually this is done in the location where you would like to install other software too.
You may see a harmless deprecation warning popping up when performing this installation, just ignore it.
"},{"location":"installation/#eb_as_module_step3","title":"Step 3: Loading the EasyBuild module","text":"Once Step 2: Using EasyBuild to install EasyBuild is completed, you should be able to load the module that was generated alongside the EasyBuild installation. You will need to do this every time you start a new shell session.
First, make the module available by running the following command (which will update the module search path environment variable $MODULEPATH):
Then, load the EasyBuild module to update your environment and make EasyBuild available for use:
Note that in this case, we don't need to make any changes to our environment for EasyBuild to work correctly. The environment module file that was generated by EasyBuild specifies all changes that need to be made.
"},{"location":"installation/#dependencies","title":"Required Dependencies","text":"This section gives further information on the required dependencies.
"},{"location":"installation/#required_shell_tools","title":"Required shell tools","text":"A couple of shell tools may be required, depending on the particular use case (in relative order of importance):
EasyBuild not only generates module files to be used along with the software it installs, it also depends on the generated modules, mainly for resolving dependencies. Hence, a modules tool must be available to consume module files with.
The path where the modules tool binary/script is located can be determined via the definition of the module function; for example, using type module or type -f module.
For modern Tcl-only environment modules (version >= 4.0.0), EasyBuild will try to fall back to finding the modulecmd.tcl binary via the $MODULES_CMD environment variable, in case modulecmd.tcl is not available in $PATH.
Since EasyBuild v4.0, no Python packages outside of the Python standard library are required.
"},{"location":"installation/#optional-dependencies","title":"Optional dependencies","text":"Some dependencies are optional and are only required to support certain features.
"},{"location":"installation/#optional_python_packages","title":"Optional Python packages","text":"EasyBuild is split up into three different packages, which are available from the Python Package Index (PyPi):
Next to these packages, a meta-package named easybuild is also available on PyPi, in order to easily install the full EasyBuild distribution.
Should the installation of EasyBuild fail for you, please open an issue to report the problems you're running into.
"},{"location":"installation/#how-to-collect-info-in-case-sanity-checks-fail-or-there-is-another-issue","title":"How to collect info in case sanity checks fail or there is another issue","text":"In order to get a better understanding in which kind of environment you are using the bootstrap script, please copy-paste the commands below and provide the output in your problem report. Do not worry if some of these commands fail or spit out error messages.
This short guide will explain how to install the standard Environment Modules software package without root permissions on a Linux or Mac OS X system, together with Tcl on which it depends.
"},{"location":"installing-environment-modules-without-root-permissions/#tcl","title":"Tcl","text":"All done! Now you are ready to build the Environment Modules package, which requires Tcl.
"},{"location":"installing-environment-modules-without-root-permissions/#environment-modules","title":"Environment Modules","text":"Alright, now just one more thing...
"},{"location":"installing-environment-modules-without-root-permissions/#set-up-your-environment","title":"Set up your environment","text":"Because you've installed Environment Modules and Tcl in a non-default location, you need to make sure your environment is setup up correctly to use them.
Since EasyBuild v4.5.0 (initial) support is available for installing extensions in parallel, that is to run the installation command for multiple extensions that are ready to install at the same time in the background, to exploit the availability of multiple cores.
Note: this is an experimental feature. Some of the mentioned functionality may be subject to change or be prone to errors.
"},{"location":"installing-extensions-in-parallel/#installing_extensions_in_parallel_configuration","title":"Configuration","text":"In addition, since the support for installing extensions in parallel is an experimental feature, the experimental configuration option must be also be enabled (see also Experimental features).
How many extension installations should be started (at maximum) at the same time is controlled by the parallel configuration option.
"},{"location":"installing-extensions-in-parallel/#installing_extensions_in_parallel_requirements","title":"Requirements","text":"For EasyBuild to be able to install a list of extensions in parallel, two requirements must be met:
There are a couple of caveats and known issues with installing extensions in parallel, which we hope to resolve in future EasyBuild releases.
This is also why the support for installing extensions in parallel is currently marked as an experimental feature.
"},{"location":"installing-extensions-in-parallel/#installing_extensions_in_parallel_caveats_known_issues_only_r","title":"Only works for R extensions","text":"The support for installing extensions in parallel currently only works for R extensions, since only the RPackage easyblock (which is used to install R packages as extensions) implements the necessary methods (see Requirements).
Supporting other types of extensions (Python, Perl, etc.) requires that the corresponding easyblocks that are used to install those extensions (like PythonPackage, PerlModule) are enhanced to support determining required dependencies and starting the installation command asynchronously.
"},{"location":"installing-extensions-in-parallel/#installing_extensions_in_parallel_caveats_known_issues_exts_list","title":"List of extensions must be self-contained","text":"The EasyBuild framework currently enforces that all required dependencies for a particular extension are included in the list of extensions that is being installed (specified via the exts_list easyconfig parameter). Extensions provided by dependencies are not taken into account (yet).
Checking which extensions are already installed for which the installation can be skipped when --skip (see Installing additional extensions using -k/-skip) is being used is still done sequentially.
Additional work is needed to also run these checks in parallel across the cores that are available to EasyBuild.
"},{"location":"installing-extensions-in-parallel/#installing_extensions_in_parallel_caveats_known_issues_sanity_check","title":"Sanity check for extensions is still run sequentially","text":"The sanity checks that are done for each extension are still done through a sequential loop over the list of extensions.
Additional work is needed to also run these checks in parallel across the cores that are available to EasyBuild.
"},{"location":"installing-lmod-without-root-permissions/","title":"Installing Lmod without root permissions","text":"This short guide will show how to install Lmod (and Lua, on which it depends) on Linux, without requiring root permissions.
"},{"location":"installing-lmod-without-root-permissions/#lua","title":"Lua","text":"Build and install Lua using the source tarball available in the Lmod SourceForge repository. This version is a lot easier to build, and already includes the required extra Lua modules. At the time of writing this relates to the lua-5.1.4.8.tar.gz tarball.
Step 1: Download and unpack lua-5.1.4.8.tar.gz.
Step 2: Configure the Lua build, provide a custom installation prefix (e.g. $HOME/lua) and specify to statically link libraries (i.e. libreadline and ncurses), to avoid problems when modules that provide these libraries are being loaded. Then build and install via make:
Dependencies: building Lmod using the steps below requires tcl, tcl-dev(el), make and bzip2
Step 1: Download and unpack the latest available Lmod version, Lmod-8.4.tar.bz2 at the time of writing.
EasyBuild provides several features that integrate with GitHub, where the different EasyBuild repositories are located.
Depending on which GitHub integration features you want to use, there are a couple of requirements:
See also Checking status of GitHub integration.
"},{"location":"integration-with-github/#github_configuration","title":"Configuration","text":"The following sections discuss the EasyBuild configuration options relevant to the GitHub integration features.
"},{"location":"integration-with-github/#github_user","title":"Providing a GitHub username","text":"A GitHub token is a string of 40 characters that is tied to your GitHub account, allowing you to access the GitHub API authenticated.
Using a GitHub token is beneficial with respect to rate limitations, and enables write permissions on GitHub (e.g. posting comments, creating gists, opening pull requests).
You will only be able to copy-paste the generated token right after you have created it. The value corresponding to an existing token can not be retrieved later through the GitHub interface.
Please keep your token secret at all times; it allows fully authenticated access to your GitHub account!
You can install the GitHub token in your keyring using EasyBuild, so it can pick it up when it needs to, using eb --install-github-token:
EasyBuild will validate the provided token, to check that authenticated access to your GitHub account works as expected.
EasyBuild will never print the full token value, to avoid leaking it. For debugging purposes, only the first and last 3 characters will be shown.
"},{"location":"integration-with-github/#github_git_working_dirs_path","title":"Specify location of working directories","text":"You can specify the location of your Git working directories with one of the following:
The provided path should be the parent directory of the location of the working directories (i.e. clones) of the EasyBuild repositories (easybuild-easyconfigs, etc.); the assumption is that you keep them all in a single parent directory.
To check the status of your setup w.r.t. GitHub integration, the --check-github command line option can be used.
Using this will trigger EasyBuild to perform a number of checks, and report back on what the test results mean for the different GitHub integration features.
If all requirements are taken care of in your setup, you should see output like this:
Checking whether push access to GitHub works may take some time, since a recent clone of the easybuild-easyconfigs GitHub repository will be created in the process (at a temporary location).
See also Requirements.
"},{"location":"integration-with-github/#github_from_pr","title":"Using easyconfigs from pull requests","text":"This can be useful to employ easyconfig files that are not available yet in the active EasyBuild installation, or to test new contributions by combining --from-pr with --upload-test-report (see Uploading test reports).
For example, to use the GCC v4.9.2 easyconfigs contributed via easyconfigs pull request #1177:
To avoid GitHub rate limiting, let EasyBuild know which GitHub account should be used to query the GitHub API, and provide a matching GitHub token; see also Installing a GitHub token.
"},{"location":"integration-with-github/#github_from_pr_vs_develop","title":"Relation between pull requests and current For open pull requests that are stable (i.e. tests pass and no merge conflicts), the pull request is effectively treated as a patch to the current develop branch. This is done to ensure that contributions that are picked up via --from-pr are correctly evaluated.
Easyconfig files touched by the pull request that are explicitly specified are then picked up from this location; see also Specifying particular easyconfig files.
"},{"location":"integration-with-github/#github_from_pr_vs_develop_merged_prs","title":"Merged pull requests","text":"Note that this implies that the easyconfig files being picked up are potentially different from the ones that appear in the specified pull request itself, taking into account that further updates may have been applied in the develop branch since the pull request got merged.
"},{"location":"integration-with-github/#github_from_pr_vs_develop_closed_unstable_prs","title":"Closed or unstable pull requests","text":"For closed and unstable pull requests, only the branch corresponding to the pull request itself is being considered, which aligns with the semantics of --from-pr as it was before EasyBuild v2.9.0. In this case, the current develop branch is not taken into account.
A pull request is considered unstable when GitHub reports merge conflicts or when GitHub Actions reports one or more failing tests.
"},{"location":"integration-with-github/#github_from_pr_robot_synergy","title":"Synergy with Since EasyBuild v1.15.0, the temporary directory containing the easyconfigs (and patch files) from the specified pull request is included in the robot search path.
Up until EasyBuild v2.9.0, this directory was prepended to the robot search path, to ensure that easyconfigs that were modified in the respective pull request are picked up via --robot when they are required. Thus, for easyconfig files that were available in the pull request as well as locally, the ones from the specified pull request were preferred.
This was changed in EasyBuild v2.9.0, where the directory containing the easyconfigs touched by the pull request is appended to the robot search path. This change was made to ensure that customized easyconfig files that are available in the robot search path are preferred over the (patched) easyconfig files from the develop branch (see also Relation between pull requests and current develop branch).
Note that the easyconfigs that are required to resolve dependencies and are available locally in $HOME/easyconfigs are being picked up as needed.
"},{"location":"integration-with-github/#github_from_pr_specifying_easyconfigs","title":"Specifying particular easyconfig files","text":"Since EasyBuid v2.0.0 the particular easyconfigs to be used can be specified, rather than using all easyconfigs that are touched by the pull request (which is the default if no easyconfigs are specified alongside --from-pr).
Again, note that locally available easyconfigs that are required to resolve dependencies are being picked up as needed.
"},{"location":"integration-with-github/#github_from_commit","title":"Using easyconfigs from a commit","text":"This can be useful to employ easyblocks that are not available yet in the active EasyBuild installation, or to test new contributions by combining --include-easyblocks-from-pr with --from-pr and --upload-test-report (see Uploading test reports).
For example, to use the LAMMPS easyblock contributed via easyblocks pull request #1964 together with the LAMMPS v7Aug2019 easyconfigs contributed via easyconfigs pull request #9884:
For every installation performed with EasyBuild, a test report is generated. By default, the test report is copied in the installation directory, right next to the log file (see also Understanding EasyBuild logs).
For each easyconfig that failed to install a partial log will be uploaded as a separate gist, and a link to this gist will be included in the test report.
The resulting test report can be viewed at https://gist.github.com/1cb2db8a2913a1b8ddbf1c6fee3ff83c .
This configuration option takes a regular expression that is used to determine which environment variables can be included in the test report (based on their name). Environment variables for which the name matches the specified regular expression will not be included in the test report.
A useful tool when reviewing pull requests for the easybuild-easyconfigs repository that add new or update existing easyconfig files is --review-pr.
The 'files' tab in the GitHub interface shows the changes being made to existing files; using --review-pr the differences with one or more other similar easyconfig files, for example the one(s) with the same toolchain (version) and/or software version, can also be evaluated.
This is very useful to quickly see how easyconfig files in pull requests differ from existing easyconfig files, and to maintain consistency across easyconfig files where desired.
The set of existing similar easyconfig files is determined by specific search criteria; the first one that results in a non-empty set of easyconfigs is retained.
The search criteria consists of a combination of the software version criterion with additional restrictions.
The software version criterion is one of the criterions below (considered in order), with x.y.z the software version of the easyconfig file from the pull request:
EasyBuild maintainers need to take the Requirements for pull requests into account.
When a PR is considered eligible for merging, EasyBuild will go ahead and merge it:
This results in the same checks being performed but skips the actual merging of the pull request, resulting in messages like:
EasyBuild provides two simple yet powerful features that make contributing to the central EasyBuild repositories significantly easier and less error-prone, especially for people who are not very familiar with git and/or GitHub yet:
It is very useful to quickly see how easyconfig files in pull requests differ from existing easyconfig files, and to maintain consistency across easyconfig files where desired.
In its simplest form, you just provide the location of the file(s) that you want to include in the pull request:
The working copy of the EasyBuild repository is created in a temporary location, and cleaned up once the pull request has been created. EasyBuild does not make changes to an existing working copy you may have in place already (cfr. Specify location of working directories).
For example, to create a pull request for a new version of, let's say, EasyBuild:
Similarly to creating new pull requests, existing pull requests can be easily updated using eb --update-pr (regardless of whether or not they were created with --new-pr).
Again, this take care of the whole procedure required to update an existing pull request:
EasyBuild will try and figure out where each patch file should be located (i.e. in the same directory as the easyconfig files that require that patch file), by scanning the provided easyconfigs (or, if needed, scanning all existing easyconfig files).
When providing one or more patch files, you must specify a (meaningful) commit message via --pr-commit-msg, see Controlling pull request metadata.
"},{"location":"integration-with-github/#github_new_update_pr_delete","title":"Deleting easyconfig files or patches","text":"Next to adding easyconfigs files or patches, or modifying existing ones, you can also specify to delete particular files, by including a colon character : before the name of the file.
You can control the metadata for pull requests using the following configuration options:
EasyBuild will use sensible defaults for each of these, see below.
"},{"location":"integration-with-github/#default-branch-name-for-new-pull-requests","title":"Default branch name for new pull requests","text":"Although there is usually no reason to change this default, it can be done if desired using --pr-branch-name when opening a new pull request with --new-pr.
"},{"location":"integration-with-github/#default-commit-message","title":"Default commit message","text":"EasyBuild will try to generate an appropriate default commit message when only new easyconfigs are being added via --new-pr.
When existing easyconfigs are being modified, patch files are being added/updated or --update-pr is used, a custom (meaningful) commit message must be provided via --pr-commit-msg (see Controlling pull request metadata).
"},{"location":"integration-with-github/#default-pull-request-description","title":"Default pull request description","text":"It is generally advised to provide more descriptive information, although the changes made by the pull request may be self-explanatory (e.g. when only adding new easyconfig files).
Particularly useful information to specify here is dependencies on other pull requests, by copy-pasting the respective URLs with a short descriptive message like 'depends on PR <URL>'.
"},{"location":"integration-with-github/#default-pull-request-title","title":"Default pull request title","text":"The pull request title is derived from the easyconfig files being changed/added, taking into account the recommendation for easyconfig pull requests to clearly specify module class, toolchain, software name/version, as follows: {<module_class>}[<toolchain>] <software_name> v<software_version>.
For example, when opening a pull request for an easyconfig for Python 2.7.11 with the intel/2016a toolchain, the default pull request title will be something like: {lang}[intel/2016a] Python v2.7.11 .
If multiple easyconfig files are provided, the respective software names/versions will be included separated by a ,, up until the first 3 easyconfig files (to avoid excessively lengthy pull request titles).
In case (only) existing easyconfig files are being changed, it's advisable to provide a more descriptive title using --pr-title.
"},{"location":"integration-with-github/#github_configuring_new_update_pr","title":"Configuring Easybuild creates a lock before starting the installation of an easyconfig file, to avoid a collision between multiple installations running at the same time.
If an EasyBuild session tries to install an easyconfig file when a lock for that installation already exists, it will be automatically aborted with an error like \"Lock ... already exists, aborting!\".
Locking of installations was implemented in EasyBuild version 4.2.0 .
"},{"location":"locks/#locks_implementation","title":"Locking implementation details","text":"Easybuild will create a lock when starting an installation if no corresponding lock exists yet, regardless of whether the installation was requested explicitly or is performed to resolve a dependency.
The name of the lock corresponds to the full path of the installation directory, with slashes (/) and dashes (-) replaced by underscores (_), and with an additional .lock added at the end.
Locks are created in the locks directory.
The lock created by EasyBuild is an empty directory (rather than a file), because that can be created more atomically on modern filesystems.
A lock is automatically removed by Easybuild when the installation ends, regardless of whether the installation was successful or not. Therefore, new installations of the same easyconfig will be aborted in case of:
If a previous installation was abruptly interrupted and a lock was left in place, it can be easily removed using the rmdir command (since the lock is actually an empty directory).
"},{"location":"locks/#locks_configuration_options","title":"Configuration options related to installation locks","text":"The behaviour of the locking mechanism in Easybuild can be tuned with the following configuration options:
"},{"location":"locks/#locks_ignore","title":"Ignoring locks","text":"Use this with caution, since installations may be (partially) overwritten if another EasyBuild session is also performing those installations!
"},{"location":"locks/#locks_wait","title":"Waiting for locks to be removed","text":"Maximum amount of time (in seconds) to wait until lock is released (0 means no waiting at all, exit with error; -1 means no waiting limit, keep waiting).
If the lock is never removed, the EasyBuild session will never terminate; it will keep checking every S seconds whether the lock is still in place.
If desired, an alternate location where locks should be created and checked for can be specified via the --locks-dir configuration option.
Keep in mind that a path on a shared filesystem should be used, to ensure that active EasyBuild sessions running on different systems use the same locks directory.
EasyBuild thoroughly keeps track of the executed build and install procedures. This page details some of the specifics, to help you making sense of them.
"},{"location":"log-files/#basic-information","title":"Basic information","text":"A separate log file is created for each build and install procedure that is performed. After each successful installation, this application log file is copied to the install directory for future reference.
By default, the application log file is copied to a subdirectory of the installation prefix named easybuild, and has a filename like easybuild-WRF-4.4.1-20230426.143346.log for example, which corresponds to the filename template easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log. This aspect can be tweaked via the --logfile-format configuration option.
Always include a reference to a log file (even if partial) when reporting a potential bug in EasyBuild. A particularly useful way of doing so is by creating a Gist (https://gist.github.com/), and sharing the corresponding URL. This is much better than sending a lengthy log file via email, since it can be easily shared across different communication channels (mailing list, IRC, IM, etc.).
"},{"location":"log-files/#navigating-log-files","title":"Navigating log files","text":"Extracting the information you're interested in from an EasyBuild log file may be a daunting task, especially for debug logs. The information and guidelines in this section should make navigating logs less scary.
"},{"location":"log-files/#log-message-format","title":"Log message format","text":"Each log message as emitted by EasyBuild follows a well-defined format. Example:
For each step performed in the build and installation process, corresponding log messages is emitted. For example:
For each executed shell command, log messages are included with the full command line, the location where the command was executed and the command's output and exit code. For example:
If you are primarily interested in the different commands as they were executed by EasyBuild, you can use INFO cmd (or run_cmd, in debug logs) as a search pattern.
Next to the configure/build/install commands, EasyBuild also runs a couple of other commands to obtain system information, or to query the modules tool. Typically, a single invocation of eb involves executing a dozen or so different shell commands, minimally.
"},{"location":"maintainers/","title":"EasyBuild maintainers","text":""},{"location":"maintainers/#maintainers_criteria","title":"Criteria","text":"The release managers are responsible for releasing new stable EasyBuild versions on a regular basis, with the help of the other EasyBuild maintainers.
Sebastian, Miguel & Kenneth have been working together to get EasyBuild releases out the door on a regular basis (about once every 6 weeks, see https://pypi.org/project/easybuild/#history).
The EasyBuild maintainers all have admin access to the different EasyBuild GitHub repositories:
A couple of different ways are available to manipulate the list of dependencies that are specified for the software packages being installed.
"},{"location":"manipulating-dependencies/#filter_deps","title":"Filtering out dependencies using To avoid that certain dependencies are being installed, a list of software names can be specified to --filter-deps. Any time a dependency with a name from this list is specified, it will be simply filtered out by EasyBuild, and thus disregarded when resolving dependencies, loading modules for the dependencies in the build environment, and including 'module load' statements in the generated module files.
This can be useful when particular tools and libraries are already provided by OS packages (or in some other way), and should not be reinstalled as modules by EasyBuild.
Since EasyBuild v3.8.0, filtering dependencies based on their version is also supported.
When a version range is specified, a lower limit and/or upper limit can be specified (separated by :). In other words, the version range can be open ended. The : separator is strictly required.
Selected software packages can be marked to be installed as hidden modules (i.e., modules that are not visible via 'module avail', but can be loaded) whenever they are included as a dependency, via the --hide-deps configuration option.
Using Lmod (version >= 5.7.5) or Environment Modules (version >= 4.6.0), hidden modules can be made visible in the output of 'module avail' using respectively the --show-hidden or --all option.
By default, EasyBuild will try to resolve dependencies using the same toolchain as the one that is used for the software being installed, unless a specific toolchain is specified for the dependency itself (see Dependencies).
When instructed to use minimal toolchains, EasyBuild will check whether an easyconfig file is available (in the robot search path, see Searching for easyconfigs: the robot search path) for that dependency using the different subtoolchains of the toolchain specified for the 'parent' software. Subtoolchains are considered 'bottom-up', i.e. starting with the most minimal subtoolchain (typically a compiler-only toolchain), and then climbing up towards the toolchain that is specified for the software being installed.
Note that if a specific toolchain is specified for a particular dependency, EasyBuild will stick to using it, even when instructed to use minimal toolchains. Also note that as of v3.0, if no easyconfig exists to resolve a dependency using the default toolchain EasyBuild will search for the dependency using a compatible subtoolchain (the difference being that the search order is from the top of the toolchain hierarchy to the bottom).
"},{"location":"manipulating-dependencies/#minimal_toolchains_system","title":"Considering You can instruct EasyBuild to take existing modules into account when determining which subtoolchain should be used for each of the dependencies, using the --use-existing-modules configuration option.
By default existing modules are ignored, meaning that the EasyBuild dependency resolution mechanism will pick a minimal toolchain for each dependency solely based on the available easyconfig files (if the --minimal-toolchains configuration option is enabled, that is).
So, for the zlib v1.2.12 dependency included in the example above, the following scenarios are possible:
Packaging support was added as an experimental feature in EasyBuild v2.2.0 (cfr. Experimental features). Since EasyBuild v2.5.0, it is considered stable.
"},{"location":"packaging-support/#packaging_prereq","title":"Prerequisites","text":"EasyBuild leverages FPM to create binary packages (RPMs, Debian files, etc.).
Hence, FPM must be available in some way or another. One way is via EasyBuild, for example by installing a module for FPM using one of the available easyconfig files.
EasyBuild will also take care of installing Ruby for you (which is required for FPM itself):
Several configuration options related to packaging support are available.
Changing the package naming scheme should be done with caution. For example, RPM will only allow one package of a particular name to be installed, so if you wish multiple versions of a package to be installed at the same time you need to ensure variables like the software version are included in the package name.
"},{"location":"packaging-support/#packaging_usage","title":"Usage","text":"To create packages for existing software installations (performed using EasyBuild), combine --package with --skip --rebuild:
Several ways of performing partial installations are supported. These may be useful when debugging a particular issue with the installation procedure being performed by EasyBuild, updating existing software installations or module files, or after changing the EasyBuild configuration (e.g., switching to module files in Lua syntax or a different module naming scheme).
"},{"location":"partial-installations/#partial_installation_stop","title":"Stopping the installation procedure after a step using To stop the installation procedure after a specific step in the installation procedure, the -s/--stop command line option can be used; the name of the step must be supplied as an argument.
It may be useful to be able to batch-download sources on a machine where no modules tool is installed. The --fetch option, which is equivalent with --stop fetch --ignore-osdeps, addresses this requirement.
For software applications that may include Extensions, it is often required to install one or more additional extensions without having to reinstall the software package (and all extensions) from scratch. For this purpose, the -k/--skip command line option is available.
To actually skip an existing software installation and all installed extensions, a corresponding module must be available already; if not, the installation procedure will be performed from scratch. To trigger the installation of missing extensions, --rebuild ( or --force, see Forced reinstallation) must be used as well; without it, the installation procedure will be skipped as a whole (since the module is already available).
i) ensure that all (extension) sources are available (and try to fetch them if needed); ii) prepare the build environment; iii) check which extensions have not been installed yet; iv) install the missing extensions; v) run the sanity check (which includes checking that all extensions are available) vi) regenerate the module file (since it contains a list of installed extensions)
Since EasyBuild v2.1, it is possible to only (re)generate the module file that matches the specifications in the easyconfig file, using --module-only. Depending on the use case, additional options should be supplied.
To only generate a module file (i.e., skip actually building and installing the software), or to regenerate an existing module file, --module-only can be used.
Generating an additional module file, next to the one(s) already available, is also supported. This can achieved by combining --module-only with additional configuration options that apply to the module generation.
A patch file, or just patch for short, is a text file that can be used to modify an existing software sources. They are often used to fix bugs, but can also be used to improve the usability or performance.
"},{"location":"patch-files/#including-patches-in-an-easyconfig-file","title":"Including patches in an easyconfig file","text":"To create a patch file to use with EasyBuild, follow the steps below.
"},{"location":"patch-files/#1-copy-unpacked-sources","title":"1) Copy unpacked sources","text":"Start by copying the unpacked sources, before making any changes, so we can determine which changes were made:
Create the patch file by comparing the original sources with the modified sources using the diff command:
Please also add a description on top of the patch file, along with the author and/or reference to the source of the patch.
EasyBuild will show progress bars for various aspects of the installation progress by default, if the Rich Python package is available.
The progress bars shown by EasyBuild are dynamic: they are only visible when they are relevant.
Note that for most progress bars each step is treated as being equal even though the time taken for the various steps varies. There are many factors that impact how long an individual installation step, installing an easyconfig, or installing an extension may take and this makes it very difficult to get a good estimate on how much time will be needed. The download progress bar is an exception here (as long as the size of the file to download could be determined first).
"},{"location":"progress-bars/#types-of-progress-bars","title":"Types of progress bars","text":"EasyBuild will show different progress bars to show the progress for different aspects of the installation process.
"},{"location":"progress-bars/#overall-progress-bar-status-bar","title":"Overall progress bar (status bar)","text":"The progress bar at the bottom, also known as the status bar, shows the overall progress in installing software for the currently active EasyBuild session.
Processed easyconfigs are shown in reversed order: most recently processed easyconfigs are listed first.
If EasyBuild is configured to continue processing easyconfigs when an installation failed (for example when using --upload-test-report), failing easyconfigs are listed before easyconfigs that were installed successfully, to highlight failing installations.
The status bar is not shown if only a single easyconfig file is being installed, and is hidden automatically as soon as the EasyBuild session finishes.
"},{"location":"progress-bars/#easyconfig-progress-bar","title":"Easyconfig progress bar","text":"A dedicated progress bar is shown for every easyconfig file that is installed, right above the status bar (if present), which shows:
The progress bar for a specific easyconfig file will be hidden as soon as the installation finishes (regardless of whether it was successful or not).
"},{"location":"progress-bars/#download-progress-bars","title":"Download progress bars","text":"When EasyBuild is downloading one or more files, a dedicated progress bar will be visible:
The download progress bars will be hidden as soon as the downloading has been completed (or has failed).
"},{"location":"progress-bars/#extensions-progress-bar","title":"Extensions progress bar","text":"When extensions are being installed for a particular easyconfig, a dedicated progress bar will pop up for the extensions step, which shows:
For information about configuring EasyBuild, see Configuring Easybuild.
"},{"location":"progress-bars/#output-style","title":"Starting with EasyBuild v4.0, the EasyBuild framework and easyblocks are compatible with both Python versions 2 and 3. More specifically, the following Python versions are currently supported:
To determine which Python version is being used to run EasyBuild, you can define the $EB_VERBOSE environment variable.
Through this approach we can hide subtle differences between Python 2 and 3, while avoiding code duplication and Python version checks throughout the codebase, as well as avoid requiring packages like six or future (which facilitate maintaining compatibility with Python 2 and 3, but are also a bit of a burden).
Function to create a metaclass that can be used as a base class, implemented in a way that is compatible with both Python 2 and 3.
"},{"location":"python-2-3-compatibility/#py2vs3_extract_method_name","title":"Function to method name from lambda function, implemented in a way that is compatible with both Python 2 and 3.
"},{"location":"python-2-3-compatibility/#py2vs3_HTTPError","title":"Function to create a wrapper base class using the specified metaclass, implemented in a way that is compatible with both Python 2 and 3.
"},{"location":"python-2-3-compatibility/#py2vs3_OrderedDict","title":"Function to raise an error with specified message and traceback, implemented in a way that is compatible with both Python 2 and 3.
"},{"location":"python-2-3-compatibility/#py2vs3_Request","title":"The latest version of EasyBuild provides support for building and installing 3,670 different software packages, including 41 different (compiler) toolchains. It contains 259 software-specific easyblocks and 43 generic easyblocks, alongside 20,670 easyconfig files.
","boost":0.5},{"location":"release-notes/#release_notes_eb494","title":"EasyBuild v4.9.4 (22 Sept 2024)","text":"