{bio}[foss/2023a] CellOracle v0.18.0, velocyto v0.17.17, genomepy v0.16.1, ...

easybuild/easyconfigs/c/CellOracle/CellOracle-0.18.0-foss-2023a.eb

@@ -0,0 +1,66 @@
+easyblock = 'PythonBundle'
+
+name = 'CellOracle'
+version = '0.18.0'
+
+homepage = 'https://github.com/morris-lab/CellOracle'
+description = """CellOracle is a Python library for in silico gene perturbation analyses using single-cell omics data
+and Gene Regulatory Network models."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('R', '4.3.2'),
+    ('SciPy-bundle', '2023.07'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('numba', '0.58.1'),
+    ('matplotlib', '3.7.2'),
+    ('Seaborn', '0.13.2'),
+    ('scikit-learn', '1.3.1'),
+    ('h5py', '3.9.0'),
+    ('velocyto', '0.17.17'),
+    ('umap-learn', '0.5.5'),
+    ('Arrow', '14.0.1'),
+    ('tqdm', '4.66.1'),
+    ('python-igraph', '0.11.4'),
+    ('IPython', '8.14.0'),
+    ('scanpy', '1.9.8'),
+    ('GOATOOLS', '1.4.5'),
+    ('genomepy', '0.16.1'),
+    ('GimmeMotifs', '0.17.2'),
+    ('anndata', '0.10.5.post1'),
+    ('python-louvain', '0.16'),
+    ('jupyter-contrib-nbextensions', '0.7.0'),
+    ('Qtconsole', '5.5.1'),
+]
+
+use_pip = True
+
+# remove louvain from requirements, since CellOracle doesn't actually use it at all
+local_preinstallopts = "sed -i '/louvain/d' requirements.txt && "
+# drop strict version requirement for matplotlib dependency
+local_preinstallopts += "sed -i 's/matplotlib.*/matplotlib/g' requirements.txt && "
+# drop strict version requirement for pandas dependency
+local_preinstallopts += "sed -i 's/pandas.*/pandas/g' requirements.txt && "
+
+
+exts_list = [
+    ('jupyter_console', '6.6.3', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'],
+    }),
+    ('jupyter', '1.0.0', {
+        'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'],
+    }),
+    ('celloracle', version, {
+        'preinstallopts': local_preinstallopts,
+        'checksums': ['a73bbdae36289748051e073409d853489a233bda90f50ab5031131b92dda2133'],
+    }),
+]
+
+sanity_check_commands = ["python -c 'import celloracle; celloracle.check_python_requirements()'"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2023a.eb

@@ -0,0 +1,81 @@
+easyblock = 'PythonBundle'
+
+name = 'GimmeMotifs'
+version = '0.17.2'
+
+homepage = 'https://github.com/vanheeringen-lab/gimmemotifs'
+description = "Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('poetry', '1.5.1')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('pybedtools', '0.9.1'),
+    ('Pysam', '0.22.0'),
+    ('scikit-learn', '1.3.1'),
+    ('Seaborn', '0.13.2'),
+    ('statsmodels', '0.14.1'),
+    ('tqdm', '4.66.1'),
+    ('genomepy', '0.16.1'),
+    ('qnorm', '0.8.1'),
+    ('Arrow', '14.0.1'),  # provides pyarrow, required by feather-format
+    ('HTSeq', '2.0.7'),  # required by biofluff
+    ('pyBigWig', '0.3.22'),  # required by biofluff
+]
+
+use_pip = True
+
+exts_list = [
+    ('palettable', '3.3.3', {
+        'checksums': ['094dd7d9a5fc1cca4854773e5c1fc6a315b33bd5b3a8f47064928facaf0490a8'],
+    }),
+    ('biofluff', '3.0.4', {
+        'modulename': 'fluff',
+        # remove pyBigWig dependency - pip_check fails with "import pybigwig"
+        'preinstallopts': "sed -i '/pyBigWig/d' setup.py && ",
+        'checksums': ['ef7b0a54103a830f197f21aa3d1ade8bdcddf613b437ea38c95260bb45324d6b'],
+    }),
+    ('diskcache', '5.6.3', {
+        'checksums': ['2c3a3fa2743d8535d832ec61c2054a1641f41775aa7c556758a109941e33e4fc'],
+    }),
+    ('feather-format', '0.4.1', {
+        'modulename': 'feather',
+        'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'],
+    }),
+    ('iteround', '1.0.4', {
+        'source_urls': ['https://github.com/cgdeboer/iteround/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['445e4f0c793ae558e4db3cdee7e23d77459b9c586e8021667aa60c14ba7ff45f'],
+    }),
+    ('logomaker', '0.8', {
+        'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'],
+    }),
+    ('loguru', '0.7.2', {
+        'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'],
+    }),
+    ('xxhash', '3.4.1', {
+        'checksums': ['0379d6cf1ff987cd421609a264ce025e74f346e3e145dd106c0cc2e3ec3f99a9'],
+    }),
+    ('xdg', '6.0.0', {
+        'checksums': ['24278094f2d45e846d1eb28a2ebb92d7b67fc0cab5249ee3ce88c95f649a1c92'],
+    }),
+    ('gimmemotifs', version, {
+        'preinstallopts': """sed -i '/"configparser"/d' setup.py && """,
+        'checksums': ['fbf70997abce6a75451c10b96994f8dbc03152b01df5cf30bf4397c98a9b54d2'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/gimme'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["gimme --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/g/genomepy/genomepy-0.16.1-foss-2023a.eb

@@ -0,0 +1,56 @@
+easyblock = 'PythonBundle'
+
+name = 'genomepy'
+version = '0.16.1'
+
+homepage = 'https://github.com/vanheeringen-lab/genomepy'
+description = "genomepy is designed to provide a simple and straightforward way to download and use genomic data"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('hatchling', '1.18.0')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('tqdm', '4.66.1'),
+    ('Biopython', '1.83'),
+    ('mygene', '3.2.2'),
+    ('pyfaidx', '0.8.1.1'),
+    ('PyYAML', '6.0'),
+    ('protobuf-python', '4.24.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('diskcache', '5.6.3', {
+        'checksums': ['2c3a3fa2743d8535d832ec61c2054a1641f41775aa7c556758a109941e33e4fc'],
+    }),
+    ('loguru', '0.7.2', {
+        'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'],
+    }),
+    ('mysql-connector-python', '8.4.0', {
+        'modulename': 'mysql.connector',
+        'sources': ['mysql_connector_python-%(version)s-py2.py3-none-any.whl'],
+        'checksums': ['35939c4ff28f395a5550bae67bafa4d1658ea72ea3206f457fff64a0fbec17e4'],
+    }),
+    ('norns', '0.1.6', {
+        'preinstallopts': "sed -i '/nose/d' setup.py && ",
+        'checksums': ['1f3c6ccbe79b2cb3076f66a352cd76462593adbabe9ebb262f879a9d0a6634e4'],
+    }),
+    (name, version, {
+        'checksums': ['22e81827acfdb4d9e6adda1f8e4cfafbb97f1c1788348e86b930c9daa51088c5'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/genomepy'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["genomepy --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.7-foss-2023a.eb

@@ -0,0 +1,43 @@
+# Updated to PythonBundle and latest version from Pypi
+# Author: J. Sassmannshausen (Imperial College London/UK)
+# Update: P.Tománek (Inuits)
+
+easyblock = 'PythonBundle'
+
+name = 'HTSeq'
+version = '2.0.7'
+
+homepage = 'https://github.com/simon-anders/htseq'
+description = """HTSeq is a Python library to facilitate processing and analysis
+ of data from high-throughput sequencing (HTS) experiments."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('SWIG', '4.1.1')]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('Pysam', '0.22.0'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('htseq', version, {
+        'modulename': 'HTSeq',
+        'checksums': ['c1490cede77fb04c8f3a9efeb44d41399cd466a6082180529e63c1dade203fdd'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s-count', 'bin/%(namelower)s-qa'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s/scripts'],
+}
+
+sanity_check_commands = ['%(namelower)s-count --help']
+
+moduleclass = 'bio'

easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2023a.eb

@@ -0,0 +1,34 @@
+# Author: Pavel Grochal (INUITS)
+# Update: Pavel Tománek (INUITS)
+# License: GPLv2
+
+easyblock = 'PythonBundle'
+
+name = 'mygene'
+version = '3.2.2'
+
+homepage = 'https://github.com/biothings/mygene.py'
+description = "Python Client for MyGene.Info services."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('biothings_client', '0.3.1', {
+        'checksums': ['c972bf2e02b6f9cc78f7f2fbc5ef02cc56fe4f8a2adcb8801ec902f4ab7011e6'],
+    }),
+    (name, version, {
+        'checksums': ['e729cabbc28cf5afb221bca1ab637883b375cb1a3e2f067587ec79f71affdaea'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2023a.eb

@@ -0,0 +1,40 @@
+easyblock = 'PythonBundle'
+
+name = 'velocyto'
+version = '0.17.17'
+
+homepage = 'https://velocyto.org/velocyto.py/'
+description = "Velocyto is a library for the analysis of RNA velocity."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('numba', '0.58.1'),
+    ('scikit-learn', '1.3.1'),
+    ('h5py', '3.9.0'),
+    ('Pysam', '0.22.0'),
+    ('loompy', '3.0.7'),
+]
+
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'checksums': ['1ad65fc53292ce1970a70bc742d73491b370038e0b0065761303e787bf7ffe39'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/velocyto'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ['velocyto']
+
+moduleclass = 'bio'