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TGenNorth · Aug 9, 2024 · 672254d · 672254d
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commit 672254d
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diff --git a/environment.yml b/environment.yml
@@ -11,6 +11,7 @@ dependencies:
   - alsa-lib=1.2.11
   - anyio=4.3.0
   - appdirs=1.4.4
+  - archspec=0.2.3
   - argon2-cffi=23.1.0
   - argon2-cffi-bindings=21.2.0
   - arrow=1.3.0
@@ -24,6 +25,7 @@ dependencies:
   - binutils_impl_linux-64=2.40
   - biom-format=2.1.15
   - bleach=6.1.0
+  - boltons=24.0.0
   - bowtie2=2.5.4
   - brotli-python=1.1.0
   - bwa=0.7.18
@@ -36,24 +38,34 @@ dependencies:
   - cairo=1.18.0
   - certifi=2024.7.4
   - cffi=1.16.0
+  - chardet=5.2.0
   - charset-normalizer=3.3.2
   - click=8.1.7
   - colorama=0.4.6
   - comm=0.2.2
+  - conda=24.7.1
+  - conda-build=24.7.1
+  - conda-index=0.5.0
+  - conda-libmamba-solver=24.7.0
   - conda-pack=0.7.0
+  - conda-package-handling=2.3.0
+  - conda-package-streaming=0.10.0
+  - conda-souschef=2.2.3
   - cryptography=42.0.7
   - curl=8.8.0
   - debugpy=1.8.1
   - decorator=4.4.2
   - defusedxml=0.7.1
   - dill=0.3.8
+  - distro=1.9.0
   - entrypoints=0.4
   - exceptiongroup=1.2.0
   - executing=2.0.1
   - expat=2.6.2
   - filelock=3.14.0
   - flake8=7.1.0
   - flufl.lock=7.1
+  - fmt=10.2.1
   - font-ttf-dejavu-sans-mono=2.37
   - font-ttf-inconsolata=3.000
   - font-ttf-source-code-pro=2.038
@@ -64,11 +76,13 @@ dependencies:
   - fqdn=1.5.1
   - freetype=2.12.1
   - fribidi=1.0.10
+  - frozendict=2.4.4
   - gcc_impl_linux-64=13.2.0
   - gfortran_impl_linux-64=13.2.0
   - giflib=5.2.2
   - globus-sdk=3.41.0
   - graphite2=1.3.13
+  - grayskull=2.3.0
   - gxx_impl_linux-64=13.2.0
   - h5py=3.11.0
   - harfbuzz=8.5.0
@@ -90,6 +104,7 @@ dependencies:
   - jedi=0.19.1
   - jinja2=3.1.4
   - joblib=1.4.2
+  - jsonpatch=1.33
   - jsonpointer=2.4
   - jsonschema=4.22.0
   - jsonschema-specifications=2023.12.1
@@ -107,6 +122,7 @@ dependencies:
   - ld_impl_linux-64=2.40
   - lerc=4.0.0
   - libaec=1.1.3
+  - libarchive=3.7.4
   - libblas=3.9.0
   - libcblas=3.9.0
   - libcups=2.3.3
@@ -127,12 +143,16 @@ dependencies:
   - libjpeg-turbo=3.0.0
   - liblapack=3.9.0
   - liblapacke=3.9.0
+  - liblief=0.14.1
+  - libmamba=1.5.8
+  - libmambapy=1.5.8
   - libnghttp2=1.58.0
   - libnsl=2.0.1
   - libopenblas=0.3.27
   - libpng=1.6.43
   - libsanitizer=13.2.0
   - libsodium=1.0.18
+  - libsolv=0.7.29
   - libsqlite=3.45.3
   - libssh2=1.11.0
   - libstdcxx-devel_linux-64=13.2.0
@@ -148,11 +168,14 @@ dependencies:
   - lxml=5.2.2
   - lz4=4.3.3
   - lz4-c=1.9.4
+  - lzo=2.10
   - make=4.3
   - markupsafe=2.1.5
   - matplotlib-inline=0.1.7
   - mccabe=0.7.0
+  - menuinst=2.1.1
   - mistune=3.0.2
+  - more-itertools=10.4.0
   - mpi=1.0
   - natsort=8.4.0
   - nbclassic=1.1.0
@@ -175,23 +198,30 @@ dependencies:
   - paramiko=3.4.0
   - parsl=2024.4.15
   - parso=0.8.4
+  - patch=2.7.6
+  - patchelf=0.17.2
   - pbzip2=1.1.13
   - pcre2=10.43
   - perl=5.32.1
   - pexpect=4.9.0
   - pickleshare=0.7.5
   - pip=24.0
   - pixman=0.43.2
+  - pkginfo=1.11.1
   - pkgutil-resolve-name=1.3.10
   - platformdirs=4.2.2
   - pluggy=1.5.0
+  - progressbar2=4.4.2
   - prometheus_client=0.20.0
   - prompt-toolkit=3.0.42
   - psutil=5.9.8
   - pthread-stubs=0.4
   - ptyprocess=0.7.0
   - pure_eval=0.2.2
+  - py-lief=0.14.1
+  - pybind11-abi=4
   - pycodestyle=2.12.0
+  - pycosat=0.6.6
   - pycparser=2.22
   - pyflakes=3.2.0
   - pygments=2.18.0
@@ -204,7 +234,9 @@ dependencies:
   - python-dateutil=2.9.0
   - python-fastjsonschema=2.19.1
   - python-json-logger=2.0.7
+  - python-libarchive-c=5.1
   - python-tzdata=2024.1
+  - python-utils=3.8.2
   - python_abi=3.9
   - pytz=2024.1
   - pyyaml=6.0.1
@@ -226,24 +258,33 @@ dependencies:
   - r-rlang=1.1.3
   - r-rprojroot=2.0.4
   - r-withr=3.0.0
+  - rapidfuzz=3.9.6
   - readline=8.2
   - referencing=0.35.1
+  - reproc=14.2.4.post0
+  - reproc-cpp=14.2.4.post0
   - requests=2.32.2
   - rfc3339-validator=0.1.4
   - rfc3986-validator=0.1.1
+  - ripgrep=14.1.0
   - rpds-py=0.18.1
+  - ruamel.yaml=0.18.6
+  - ruamel.yaml.clib=0.2.8
+  - ruamel.yaml.jinja2=0.2.4
   - samtools=1.20
   - scikit-bio=0.6.0
   - scikit-learn=1.4.2
   - scipy=1.13.0
   - sed=4.8
+  - semver=2.13.0
   - send2trash=1.8.3
   - setproctitle=1.3.3
   - setuptools=70.0.0
   - six=1.16.0
   - sniffio=1.3.1
   - soupsieve=2.5
   - stack_data=0.6.2
+  - stdlib-list=0.10.0
   - sysroot_linux-64=2.12
   - tbb=2021.12.0
   - tblib=3.0.0
@@ -253,8 +294,10 @@ dependencies:
   - tk=8.6.13
   - tktable=2.10
   - tomli=2.0.1
+  - tomli-w=1.0.0
   - tomlkit=0.12.5
   - tornado=6.4.1
+  - tqdm=4.66.5
   - traitlets=5.9.0
   - typeguard=4.2.1
   - types-python-dateutil=2.9.0.20240316
@@ -267,6 +310,7 @@ dependencies:
   - unifrac-binaries=1.4
   - uri-template=1.3.0
   - urllib3=2.2.1
+  - versioneer=0.29
   - wcwidth=0.2.13
   - webcolors=1.13
   - webencodings=0.5.1
@@ -293,12 +337,15 @@ dependencies:
   - xorg-xproto=7.0.31
   - xz=5.2.6
   - yaml=0.2.5
+  - yaml-cpp=0.8.0
   - zeromq=4.3.5
   - zipp=3.17.0
   - zlib=1.2.13
+  - zstandard=0.23.0
   - zstd=1.5.6
   - pip:
       - pysam==0.22.1
-      - git+https://github.com/TGenNorth/q2-aligners#egg=samUpdates
-      - git+https://github.com/TGenNorth/q2-nasp2-types#egg=bamUpdates
-      - git+https://github.com/TGenNorth/q2-trimmers
+      - q2-aligners==0.0.3.dev24+g020ed09
+      - q2-nasp2-types==0.0.5.dev8
+      - q2-trimmers==0+untagged.28.g1ca5334.dirty
+prefix: /home/nsylvester/miniconda3/envs/qiime2-q2-asap