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Add PySCENIC (#50445)
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* Delete recipes/pyscenic/build.sh

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* deleting packeges from conda

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---------

Co-authored-by: Pablo Moreno <[email protected]>
Co-authored-by: mencian <[email protected]>
Co-authored-by: Joshua Zhuang <[email protected]>
Co-authored-by: Alicia A. Evans <[email protected]>
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5 people authored Oct 29, 2024
1 parent f388436 commit c055794
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11 changes: 11 additions & 0 deletions recipes/pyscenic/dill_patch.patch
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--- pyscenic-0.12.1/src/pyscenic/prune.py 2022-11-21 10:38:05.000000000 +0000
+++ pyscenic-0.12.1/src/pyscenic/prune.py 2024-10-02 10:20:58.423708208 +0000
@@ -20,8 +20,8 @@
from dask import delayed
from dask.dataframe import from_delayed
from dask.distributed import Client, LocalCluster
-from multiprocessing_on_dill.connection import Pipe
-from multiprocessing_on_dill.context import Process
+from multiprocessing import Pipe
+from multiprocessing import Process

80 changes: 80 additions & 0 deletions recipes/pyscenic/meta.yaml
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{% 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 }}"
patches:
- dill_patch.patch

build:
number: 0
noarch: python
entry_points:
- pyscenic = pyscenic.cli.pyscenic:main
- db2feather = pyscenic.cli.db2feather:main
- csv2loom = pyscenic.cli.csv2loom:main
- invertdb = pyscenic.cli.invertdb:main
- gmt2regions = pyscenic.cli.gmt2regions:main
run_exports:
- "{{ pin_subpackage(name, max_pin='x.x') }}"
script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"

requirements:
host:
- python >=3.6
- pip
- setuptools
run:
- python >=3.6
- aiohttp
- arboreto
- attrs
- boltons
- cloudpickle
- cytoolz
- dill
- dask-core >=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
- ctxcore

test:
imports:
- pyscenic

about:
home: "https://github.com/aertslab/pySCENIC"
summary: "Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments."
license: "GPL-3.0-or-later"
license_family: GPL3
license_file: "LICENSE.txt"
dev_url: "https://github.com/aertslab/pySCENIC"
doc_url: "https://scenic.aertslab.org"

extra:
identifiers:
- doi:10.1038/nmeth.4463
- doi:10.1038/s41592-023-01938-4
- biotools:scenic

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