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Add PySCENIC #50445
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Add PySCENIC #50445
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Original file line number | Diff line number | Diff line change |
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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 multiprocessing_on_dill-3.5.0a4 ctxcore-0.2.0; do | ||
pushd ${SRC_DIR}/${package} | ||
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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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Original file line number | Diff line number | Diff line change |
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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 | ||
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- url: "https://github.com/aertslab/ctxcore/archive/refs/tags/0.2.0.tar.gz" | ||
sha256: "a7ebf0f2625641b76a390993e12042e92fff7d0ac242c7fad5e3bff3ff3cd67a" | ||
folder: ctxcore-0.2.0 | ||
- url: "https://files.pythonhosted.org/packages/source/m/multiprocessing_on_dill/multiprocessing_on_dill-3.5.0a4.tar.gz" | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. As I mentioned above, the licensing for There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. 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. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. 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 | ||
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build: | ||
number: 0 | ||
run_exports: | ||
- "{{ pin_subpackage(name, max_pin='x.x') }}" | ||
script_env: | ||
- CONDA_BUILD_SYSROOT=/opt/conda/envs/sysroot | ||
build_args: | ||
- "-j2" | ||
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requirements: | ||
build: | ||
- "{{ compiler('c') }}" | ||
- "{{ compiler('cxx') }}" | ||
- make | ||
- python >=3.10,<3.11 | ||
- pip | ||
- setuptools | ||
- wheel | ||
- setuptools_scm | ||
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host: | ||
- python >=3.10,<3.11 | ||
- pip | ||
- setuptools | ||
- wheel | ||
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run: | ||
- python >=3.10,<3.11 | ||
- aiohttp | ||
- arboreto | ||
- attrs | ||
- boltons | ||
- cloudpickle | ||
- cytoolz | ||
- dill | ||
- dask >=2023.4.1 | ||
- distributed >=2023.4.1,<2023.5.0 | ||
- 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 | ||
- interlap | ||
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 | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. What does this number refer to? There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. it was my github id, deleted it |
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ctxcore
is in bioconda, so you should be able to add that to the dependenciesThere was a problem hiding this comment.
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agreed!