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Add PySCENIC #50445

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18 changes: 18 additions & 0 deletions recipes/pyscenic/build.sh
Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
#!/bin/bash
set -ex

if [ -z "${PYTHON}" ]; then
PYTHON=$(which python)
fi

for package in multiprocessing_on_dill-3.5.0a4 ctxcore-0.2.0; do
pushd ${SRC_DIR}/${package}

${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv
popd
done

pushd ${SRC_DIR}/pyscenic-0.12.1
${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv
popd

87 changes: 87 additions & 0 deletions recipes/pyscenic/meta.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,87 @@
{% set name = "pyscenic" %}
{% set version = "0.12.1" %}
{% set sha256 = "ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2" %}

package:
name: "{{ name|lower }}"
version: "{{ version }}"

source:
- url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
sha256: "{{ sha256 }}"
folder: pyscenic-0.12.1

- url: "https://github.com/aertslab/ctxcore/archive/refs/tags/0.2.0.tar.gz"
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ctxcore is in bioconda, so you should be able to add that to the dependencies

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agreed!

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"
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As I mentioned above, the licensing for multiprocessing_on_dill has to be worked out. It should be added to conda-forge rather than bioconda because it's not bioinformatics related.

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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

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Thanks, I see your point. I will get some clarity on this from the core team.

sha256: "d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7"
folder: multiprocessing_on_dill-3.5.0a4

build:
number: 0
run_exports:
- "{{ pin_subpackage(name, max_pin='x.x') }}"
script_env:
- CONDA_BUILD_SYSROOT=/opt/conda/envs/sysroot
build_args:
- "-j2"

requirements:
build:
- "{{ compiler('c') }}"
- "{{ compiler('cxx') }}"
- make
- python >=3.10,<3.11
- pip
- setuptools
- wheel
- setuptools_scm

host:
- python >=3.10,<3.11
- pip
- setuptools
- wheel

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

about:
home: https://github.com/aertslab/pySCENIC
summary: 'pySCENIC is a python implementation of the SCENIC pipeline'
license: MIT
license_family: MIT

extra:
recipe-maintainers:
- 179018299
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What does this number refer to?

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it was my github id, deleted it