Merge pull request #17507 from boegel/20230311000530_new_pr_CellOracle0120

{bio}[foss/2022a] CellOracle v0.12.0, GimmeMotifs v0.17.2, qnorm v0.8.1, Qtconsole v5.4.0 w/ Python 3.10.4

Author: verdurin

easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb

@@ -0,0 +1,59 @@
+easyblock = 'PythonBundle'
+
+name = 'CellOracle'
+version = '0.12.0'
+
+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': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('R', '4.2.1'),
+    ('SciPy-bundle', '2022.05'),
+    ('numba', '0.56.4'),
+    ('matplotlib', '3.5.2'),
+    ('Seaborn', '0.12.1'),
+    ('scikit-learn', '1.1.2'),
+    ('h5py', '3.7.0'),
+    ('velocyto', '0.17.17'),
+    ('umap-learn', '0.5.3'),
+    ('Arrow', '8.0.0'),
+    ('tqdm', '4.64.0'),
+    ('igraph', '0.10.3'),
+    ('IPython', '8.5.0'),
+    ('scanpy', '1.9.1'),
+    ('GOATOOLS', '1.3.1'),
+    ('genomepy', '0.15.0'),
+    ('GimmeMotifs', '0.17.2'),
+    ('Qtconsole', '5.4.0'),
+]
+
+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 gimmemotifs dependency
+local_preinstallopts += "sed -i 's/gimmemotifs.*/gimmemotifs/g' requirements.txt && "
+
+exts_list = [
+    ('jupyter-console', '6.4.4', {
+        'sources': ['jupyter_console-%(version)s.tar.gz'],
+        'checksums': ['172f5335e31d600df61613a97b7f0352f2c8250bbd1092ef2d658f77249f89fb'],
+    }),
+    ('jupyter', '1.0.0', {
+        'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'],
+    }),
+    ('celloracle', version, {
+        'checksums': ['9d533ee3e8c14828b6859ea195e92d184b050b0782fee430eda3b01359a564d5'],
+        'preinstallopts': local_preinstallopts,
+    }),
+]
+
+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-2022a.eb

@@ -0,0 +1,77 @@
+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': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('matplotlib', '3.5.2'),
+    ('pybedtools', '0.9.0'),
+    ('Pysam', '0.19.1'),
+    ('scikit-learn', '1.1.2'),
+    ('Seaborn', '0.12.1'),
+    ('statsmodels', '0.13.1'),
+    ('tqdm', '4.64.0'),
+    ('genomepy', '0.15.0'),
+    ('qnorm', '0.8.1'),
+    ('Arrow', '8.0.0'),  # provides pyarrow, required by feather-format
+    ('HTSeq', '2.0.2'),  # required by biofluff
+    ('pyBigWig', '0.3.18'),  # required by biofluff
+]
+
+use_pip = True
+
+exts_list = [
+    ('palettable', '3.3.0', {
+        'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'],
+    }),
+    ('biofluff', '3.0.4', {
+        'modulename': 'fluff',
+        'checksums': ['ef7b0a54103a830f197f21aa3d1ade8bdcddf613b437ea38c95260bb45324d6b'],
+    }),
+    ('diskcache', '5.4.0', {
+        'checksums': ['8879eb8c9b4a2509a5e633d2008634fb2b0b35c2b36192d89655dbde02419644'],
+    }),
+    ('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', '0.6.0', {
+        'checksums': ['066bd06758d0a513e9836fd9c6b5a75bfb3fd36841f4b996bc60b547a309d41c'],
+    }),
+    ('xxhash', '3.2.0', {
+        'checksums': ['1afd47af8955c5db730f630ad53ae798cf7fae0acb64cebb3cf94d35c47dd088'],
+    }),
+    ('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/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb

@@ -0,0 +1,31 @@
+easyblock = 'PythonPackage'
+
+name = 'Qtconsole'
+version = '5.4.0'
+
+homepage = 'https://jupyter.org/'
+description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media 
+output, session export, and more.
+The Qtconsole is a very lightweight application that largely feels like a       
+terminal, but provides a number of enhancements only possible in a GUI, such as 
+inline figures, proper multiline editing with syntax highlighting, graphical    
+calltips, and more."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['57748ea2fd26320a0b77adba20131cfbb13818c7c96d83fafcb110ff55f58b35']
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('IPython', '8.5.0'),
+    ('QtPy', '2.3.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'vis'

easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb

@@ -0,0 +1,36 @@
+easyblock = 'PythonPackage'
+
+name = 'qnorm'
+version = '0.8.1'
+
+homepage = 'https://github.com/Maarten-vd-Sande/qnorm'
+description = "Fast-ish (and correct!) quantile normalization in Python"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('numba', '0.56.4'),
+]
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['61b2f3ef09a9c552a4f3b83dc438cb13f191fa190164361a3a508c4777eed3c7']
+
+download_dep_fail = True
+use_pip = True
+
+# pyproject.toml included in qnorm source tarball does not include standard fields,
+# it's only there to be read by setup.py...
+preinstallopts = "sed -i 's/pyproject.toml/pyproject.toml_/g' setup.py && mv pyproject.toml pyproject.toml_ && "
+
+sanity_check_paths = {
+    'files': ['bin/qnorm'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["qnorm --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'