Add PySCENIC #50445
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| #!/bin/bash | ||
| set -ex | ||
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| if [ -z "${PYTHON}" ]; then | ||
| PYTHON=$(which python) | ||
| fi | ||
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| for package in arboreto-0.1.6 interlap-0.2.7 multiprocessing_on_dill-3.5.0a4 ctxcore-0.2.0; do | ||
| pushd ${SRC_DIR}/${package} | ||
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| if [ "$package" == "arboreto-0.1.6" ] && [ ! -f requirements.txt ]; then | ||
| echo "dask[complete]" > requirements.txt | ||
| echo "distributed" >> requirements.txt | ||
| echo "numpy>=1.16.5" >> requirements.txt | ||
| echo "pandas" >> requirements.txt | ||
| echo "scikit-learn" >> requirements.txt | ||
| echo "scipy" >> requirements.txt | ||
| fi | ||
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| ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv | ||
| popd | ||
| done | ||
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| pushd ${SRC_DIR}/pyscenic-0.12.1 | ||
| ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv | ||
| popd |
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| {% set name = "pyscenic" %} | ||
| {% set version = "0.12.1" %} | ||
| {% set sha256 = "ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2" %} | ||
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| package: | ||
| name: "{{ name|lower }}" | ||
| version: "{{ version }}" | ||
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| source: | ||
| - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" | ||
| sha256: "{{ sha256 }}" | ||
| folder: pyscenic-0.12.1 | ||
| - url: "https://files.pythonhosted.org/packages/source/a/arboreto/arboreto-0.1.6.tar.gz" | ||
| sha256: "32fdac5e8a3e0ef2e196b5827f067d815ac4e689d2fca0dc437f42abdeeb89ab" | ||
| folder: arboreto-0.1.6 | ||
| - url: "https://files.pythonhosted.org/packages/source/i/interlap/interlap-0.2.7.tar.gz" | ||
| sha256: "31e4f30c54b067c4939049f5d8131ae5e2fa682ec71aa56f89c0e5b900806ec9" | ||
| folder: interlap-0.2.7 | ||
| - url: "https://files.pythonhosted.org/packages/source/m/multiprocessing_on_dill/multiprocessing_on_dill-3.5.0a4.tar.gz" | ||
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There was a problem hiding this comment. As I mentioned above, the licensing for There was a problem hiding this comment. Working out a license like that could take a long time, in the meantime this could be used like this and possibly improved once that is resolved. There are many packages in bioconda that recourse to pip installing dependencies that are not available in conda, for instance https://github.com/bioconda/bioconda-recipes/blob/def3a07b68330abb40f7650b3747b8bee189ab66/recipes/latch/build.sh There was a problem hiding this comment. Thanks, I see your point. I will get some clarity on this from the core team. |
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| sha256: "d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7" | ||
| folder: multiprocessing_on_dill-3.5.0a4 | ||
| - url: "https://github.com/aertslab/ctxcore/archive/refs/tags/0.2.0.tar.gz" | ||
| sha256: "a7ebf0f2625641b76a390993e12042e92fff7d0ac242c7fad5e3bff3ff3cd67a" | ||
| folder: ctxcore-0.2.0 | ||
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| build: | ||
| number: 0 | ||
| run_exports: | ||
| - "{{ pin_subpackage(name, max_pin='x.x') }}" | ||
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| requirements: | ||
| build: | ||
| - "{{ compiler('c') }}" | ||
| - "{{ compiler('cxx') }}" | ||
| - make | ||
| - python >=3.10,<3.11 # Pinning Python version to 3.10 | ||
| - pip | ||
| - setuptools | ||
| - wheel | ||
| - setuptools_scm | ||
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| host: | ||
| - python >=3.10,<3.11 # Pinning Python version to 3.10 | ||
| - pip | ||
| - setuptools | ||
| - wheel | ||
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| run: | ||
| - python >=3.10,<3.11 # Pinning Python version to 3.10 | ||
| - aiohttp | ||
| - attrs | ||
| - boltons | ||
| - cloudpickle | ||
| - cytoolz | ||
| - dill | ||
| - dask | ||
| - distributed | ||
| - frozendict | ||
| - fsspec | ||
| - llvmlite | ||
| - loompy | ||
| - networkx | ||
| - numba >=0.51.2 | ||
| - numexpr | ||
| - pandas >=1.3.5 | ||
| - pyyaml | ||
| - requests | ||
| - scikit-learn | ||
| - scipy | ||
| - tqdm | ||
| - umap-learn | ||
| - numpy ==1.23.5 | ||
| - pyarrow | ||
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| test: | ||
| imports: | ||
| - pyscenic | ||
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| about: | ||
| home: https://github.com/aertslab/pySCENIC | ||
| summary: 'pySCENIC is a python implementation of the SCENIC pipeline' | ||
| license: MIT | ||
| license_family: MIT | ||
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| extra: | ||
| recipe-maintainers: | ||
| - 179018299 | ||
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There was a problem hiding this comment. What does this number refer to? There was a problem hiding this comment. it was my github id, deleted it |
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@LiliyaBioinf arboreto is available from conda, and as such should be used as a conda dependency. Can you remove it from the sources and add under requirements.run please? Can you do the same with any of the above sources that might also be in conda (usually searching for conda + name of the package should allow you to find them if the exists as conda packages). Thanks!
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https://anaconda.org/bioconda/arboreto
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and of course, if added to the requirements, then shouldn't go in the
build.sh.There was a problem hiding this comment.
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Looks like there was some discussion a while back to add multiprocessing_on_dill to conda-forge , but the upstream maintainers did not approve the PR to add the license. That would need to be resolved in some way so it can be added to conda-forge.
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maybe in the meantime multiprocessing_on_dill can be installed through pip so that the community can benefit soon from the pyscenic recipe.