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{tools}[foss/2024a] snakemake v8.27.0 #22141

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a51357d
adding easyconfigs: snakemake-8.27.0-foss-2024a.eb
Jan 9, 2025
b811390
Update easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb
asp8200 Jan 9, 2025
2d924d2
Removing redundant Cython from dependencies to builddependencies
Jan 9, 2025
71ef70e
Upgrading dependency IPython to v8.28.0
Jan 9, 2025
adb3420
Upgrading dependency wrapt to v1.16.0
Jan 9, 2025
aec7e7e
Adding new easyconfig PuLP-2.8.0-foss-2024a.eb
Jan 10, 2025
dda7ff9
Adding new easyconfig Cbc-2.10.12-foss-2024a.eb
Jan 10, 2025
0fbc9cb
Adding new easyconfig SCOTCH-7.0.6-gompi-2024a.eb
Jan 10, 2025
2477869
Updating Cbc-2.10.12-foss-2024a.eb
Jan 10, 2025
e8b3603
Updating MUMPS-5.7.2-foss-2024a-metis.eb
Jan 10, 2025
2721934
Update easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb
asp8200 Jan 10, 2025
ecc8375
Adding new easyconfig CoinUtils-2.11.12-GCC-13.3.0.eb
Jan 10, 2025
bc5541e
Adding new easyconfig Osi-0.108.11-GCC-13.3.0.eb
Jan 10, 2025
df145eb
Adding new easyconfig Clp-1.17.10-foss-2024a.eb
Jan 10, 2025
a7a5622
Breaking up line for configopts in Clp-1.17.10-foss-2024a.eb
Jan 10, 2025
5a3effc
Updating some dependencies in Cbc-2.10.12-foss-2024a.eb
Jan 10, 2025
0ccb637
Adding easyconfig for Cgl-0.60.8-foss-2024a.eb
Jan 10, 2025
d3bf2e7
Reducing line length in Clp-1.17.10-foss-2024a.eb and Osi-0.108.11-GC…
Jan 10, 2025
aea95f1
Update CoinUtils-2.11.12-GCC-13.3.0.eb
ocaisa Jan 10, 2025
926af35
Update Clp-1.17.10-foss-2024a.eb
ocaisa Jan 10, 2025
2b3e4b2
Update Osi-0.108.11-GCC-13.3.0.eb
ocaisa Jan 10, 2025
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46 changes: 46 additions & 0 deletions easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
easyblock = 'ConfigureMake'

name = 'Cbc'
version = '2.10.12'

homepage = 'https://github.com/coin-or/Cbc'
description = """Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming
solver written in C++. It can be used as a callable library or using a
stand-alone executable."""

toolchain = {'name': 'foss', 'version': '2024a'}
toolchainopts = {'pic': True, 'usempi': True}

source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases']
sources = ['%(version)s.tar.gz']
checksums = ['9ed71e4b61668462fc3794c102e26b4bb01a047efbbbcbd69ae7bde1f04f46a8']

builddependencies = [
('Autotools', '20231222'),
('Doxygen', '1.11.0'),
('pkgconf', '2.2.0'),
]
dependencies = [
('METIS', '5.1.0'),
('MUMPS', '5.7.2', '-metis'),
('CoinUtils', '2.11.10'),
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('Osi', '0.108.9'),
('Clp', '1.17.9'),
('Cgl', '0.60.8'),
('bzip2', '1.0.8'),
('zlib', '1.3.1'),
]

# Use BLAS/LAPACK from toolchain
configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --with-metis-lib="-lmetis" --with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" --without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data --with-clp-lib="-lOsiClp -lClpSolver -lClp" --with-clp-datadir=$EBROOTCLP/share/coin/Data --with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data --with-cgl-lib="-lCgl" --with-cgl-datadir=$EBROOTCGL/share/coin/Data '
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sanity_check_paths = {
'files': ['bin/%(namelower)s', 'lib/libCbc.so', 'lib/libCbcSolver.so', 'lib/libOsiCbc.so'],
'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'],
}

# other coin-or projects expect <header.hpp> instead of <coin/header.hpp>
modextrapaths = {'CPATH': 'include/coin'}

moduleclass = 'math'
27 changes: 27 additions & 0 deletions easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2024a-metis.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,27 @@
name = 'MUMPS'
version = '5.7.2'
versionsuffix = '-metis'

homepage = 'https://graal.ens-lyon.fr/MUMPS/'
description = "A parallel sparse direct solver"

toolchain = {'name': 'foss', 'version': '2024a'}
toolchainopts = {'pic': True, 'usempi': True}

source_urls = ['http://mumps-solver.org/']
sources = ['%(name)s_%(version)s.tar.gz']
checksums = ['1362d377ce7422fc886c55212b4a4d2c381918b5ca4478f682a22d0627a8fbf8']

dependencies = [
('SCOTCH', '7.0.6'),
('METIS', '5.1.0'),
]

parallel = 1

# fix 'Type mismatch between actual argument' errors with GCC 10.x
prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && '

buildopts = 'all SONAME_VERSION="%(version)s"'

moduleclass = 'math'
35 changes: 35 additions & 0 deletions easybuild/easyconfigs/p/PuLP/PuLP-2.8.0-foss-2024a.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
# Contribution by
# DeepThought, Flinders University
# R.QIAO <[email protected]>
# Updated: Petr Král (INUITS)

easyblock = 'PythonPackage'

name = 'PuLP'
version = '2.8.0'

homepage = 'https://github.com/coin-or/pulp'
description = """
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.
"""

toolchain = {'name': 'foss', 'version': '2024a'}

sources = [SOURCE_TAR_GZ]
checksums = ['4903bf96110bbab8ed2c68533f90565ebb76aa367d9e4df38e51bf727927c125']

dependencies = [
('Python', '3.12.3'),
('GLPK', '5.0'),
('Cbc', '2.10.12'),
# Gurobi requires a seperate license
# ('Gurobi', '9.5.0'),
]

download_dep_fail = True
sanity_pip_check = True
use_pip = True

moduleclass = 'tools'
25 changes: 25 additions & 0 deletions easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
name = 'SCOTCH'
version = '7.0.6'

homepage = 'https://www.labri.fr/perso/pelegrin/scotch/'
description = """Software package and libraries for sequential and parallel graph partitioning,
static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning."""

toolchain = {'name': 'gompi', 'version': '2024a'}
toolchainopts = {'pic': True}

source_urls = ['https://gitlab.inria.fr/%(namelower)s/%(namelower)s/-/archive/v%(version)s/']
sources = ['%(namelower)s-v%(version)s.tar.gz']
checksums = ['b44acd0d2f53de4b578fa3a88944cccc45c4d2961cd8cefa9b9a1d5431de8e2b']

builddependencies = [
('Bison', '3.8.2'),
('flex', '2.6.4'),
]
dependencies = [
('zlib', '1.3.1'),
]

threadedmpi = False

moduleclass = 'math'
149 changes: 149 additions & 0 deletions easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,149 @@
easyblock = 'PythonBundle'

name = 'snakemake'
version = '8.27.0'

homepage = 'https://snakemake.readthedocs.io'
description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses."

toolchain = {'name': 'foss', 'version': '2024a'}

builddependencies = [
('poetry', '1.8.3'),
('Cython', '3.0.10'),
]
dependencies = [
('Python', '3.12.3'),
('Python-bundle-PyPI', '2024.06'),
('SciPy-bundle', '2024.05'),
('GitPython', '3.1.43'),
('IPython', '8.28.0'),
('PyYAML', '6.0.2'),
('wrapt', '1.16.0'),
('PuLP', '2.8.0'),
]

sanity_pip_check = True
use_pip = True

exts_list = [
('datrie', '0.8.2', {
'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'],
}),
('plac', '1.4.3', {
'checksums': ['d4cb3387b2113a28aebd509433d0264a4e5d9bb7c1a86db4fbd0a8f11af74eb3'],
}),
('dpath', '2.2.0', {
'checksums': ['34f7e630dc55ea3f219e555726f5da4b4b25f2200319c8e6902c394258dd6a3e'],
}),
('yte', '1.5.5', {
'checksums': ['2c49831859f3216f313a17688900690872e05f8fbe77cb5d151bdb896357d57e'],
}),
('toposort', '1.10', {
'checksums': ['bfbb479c53d0a696ea7402601f4e693c97b0367837c8898bc6471adfca37a6bd'],
}),
('throttler', '1.2.2', {
'checksums': ['d54db406d98e1b54d18a9ba2b31ab9f093ac64a0a59d730c1cf7bb1cdfc94a58'],
}),
('stopit', '1.1.2', {
'checksums': ['f7f39c583fd92027bd9d06127b259aee7a5b7945c1f1fa56263811e1e766996d'],
}),
('ConfigArgParse', '1.7', {
'checksums': ['e7067471884de5478c58a511e529f0f9bd1c66bfef1dea90935438d6c23306d1'],
}),
('argparse-dataclass', '2.0.0', {
'modulename': 'argparse_dataclass',
'source_tmpl': 'argparse_dataclass-%(version)s.tar.gz',
'checksums': ['09ab641c914a2f12882337b9c3e5086196dbf2ee6bf0ef67895c74002cc9297f'],
}),
('snakemake-interface-common', '1.17.4', {
'modulename': 'snakemake_interface_common',
'source_tmpl': 'snakemake_interface_common-%(version)s.tar.gz',
'checksums': ['c2142e1b93cbc18c2cf41d15968ba8688f60b077c8284e5de057cccfc215d4d3'],
}),
('reretry', '0.11.8', {
'checksums': ['f2791fcebe512ea2f1d153a2874778523a8064860b591cd90afc21a8bed432e3'],
}),
('snakemake-interface-storage-plugins', '3.3.0', {
'modulename': 'snakemake_interface_storage_plugins',
'source_tmpl': 'snakemake_interface_storage_plugins-%(version)s.tar.gz',
'checksums': ['203d8f794dfb37d568ad01a6c375fa8beac36df8e488c0f9b9f75984769c362a'],
}),
('snakemake-interface-report-plugins', '1.1.0', {
'modulename': 'snakemake_interface_report_plugins',
'source_tmpl': 'snakemake_interface_report_plugins-%(version)s.tar.gz',
'checksums': ['b1ee444b2fca51225cf8a102f8e56633791d01433cd00cf07a1d9713a12313a5'],
}),
('snakemake-interface-executor-plugins', '9.3.3', {
'modulename': 'snakemake_interface_executor_plugins',
'source_tmpl': 'snakemake_interface_executor_plugins-%(version)s.tar.gz',
'checksums': ['11e59af04bf00e9aaee7f0b99f9358910becfccdad7b18a455d37601f6d8d2ea'],
}),
('smart-open', '7.1.0', {
'sources': ['smart_open-%(version)s.tar.gz'],
'checksums': ['a4f09f84f0f6d3637c6543aca7b5487438877a21360e7368ccf1f704789752ba'],
}),
('jupyter-core', '5.7.2', {
'modulename': 'jupyter_core',
'source_tmpl': 'jupyter_core-%(version)s.tar.gz',
'checksums': ['aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9'],
}),
('fastjsonschema', '2.19.1', {
'checksums': ['e3126a94bdc4623d3de4485f8d468a12f02a67921315ddc87836d6e456dc789d'],
}),
('nbformat', '5.10.4', {
'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
'checksums': ['3b48d6c8fbca4b299bf3982ea7db1af21580e4fec269ad087b9e81588891200b'],
}),
('immutables', '0.21', {
'checksums': ['b55ffaf0449790242feb4c56ab799ea7af92801a0a43f9e2f4f8af2ab24dfc4a'],
}),
('humanfriendly', '10.0', {
'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'],
}),
('connection-pool', '0.0.3', {
'sources': ['connection_pool-%(version)s.tar.gz'],
'checksums': ['bf429e7aef65921c69b4ed48f3d48d3eac1383b05d2df91884705842d974d0dc'],
}),
('conda-inject', '1.3.2', {
'sources': ['conda_inject-%(version)s.tar.gz'],
'checksums': ['0b8cde8c47998c118d8ff285a04977a3abcf734caf579c520fca469df1cd0aac'],
}),
(name, version, {
'checksums': ['7bee7e4f255fd75738b6840c3453c9b5a4f33c628705c38a5a462db008f0334d'],
}),
('snakemake-executor-plugin-slurm-jobstep', '0.2.1', {
'modulename': 'snakemake_executor_plugin_slurm_jobstep',
'source_tmpl': 'snakemake_executor_plugin_slurm_jobstep-%(version)s.tar.gz',
'checksums': ['58894d52b5998a34fa6f60ec511ff0bfde4a9ec96714bcaa3cd2f46cf8a33859'],
}),
('snakemake-executor-plugin-flux', '0.1.1', {
'modulename': 'snakemake_executor_plugin_flux',
'source_tmpl': 'snakemake_executor_plugin_flux-%(version)s.tar.gz',
'checksums': ['26655bd1cf5d7db5dfcfdfbd006c1db35968c0ad1772e0b010e64e6f71b00163'],
}),
('snakemake-executor-plugin-slurm', '0.12.0', {
'modulename': 'snakemake_executor_plugin_slurm',
'source_tmpl': 'snakemake_executor_plugin_slurm-%(version)s.tar.gz',
'checksums': ['7069590060e914afcd608c75aee8ccf1128f662dda3e258a84f3c83302232763'],
}),
('snakemake-executor-plugin-cluster-sync', '0.1.4', {
'modulename': 'snakemake_executor_plugin_cluster_sync',
'source_tmpl': 'snakemake_executor_plugin_cluster_sync-%(version)s.tar.gz',
'checksums': ['6a6dcb2110d4c2ee74f9a48ea68e0fd7ddd2800672ebef00a01faa4affa835ad'],
}),
('snakemake-executor-plugin-cluster-generic', '1.0.9', {
'modulename': 'snakemake_executor_plugin_cluster_generic',
'source_tmpl': 'snakemake_executor_plugin_cluster_generic-%(version)s.tar.gz',
'checksums': ['ad0dc2d8bde7d4f336364bebe11a3b2209653c481ce8fbb0ae8bec81016a9a14'],
}),
]

sanity_check_paths = {
'files': ['bin/%(name)s'],
'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'],
}

sanity_check_commands = ['%(name)s --help']

moduleclass = 'tools'
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