{bio}[foss/2022b] Compass v2024.04, python-libsbml v5.20.2, anndata v0.10.6

easybuild/easyconfigs/a/anndata/anndata-0.10.6-foss-2022b.eb

@@ -0,0 +1,43 @@
+easyblock = 'PythonBundle'
+
+name = 'anndata'
+version = '0.10.6'
+
+homepage = 'https://github.com/scverse/anndata'
+description = """anndata is a Python package for handling annotated data matrices in memory and on disk,
+ positioned between pandas and xarray"""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('h5py', '3.8.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('packaging', '23.2', {
+        'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'],
+    }),
+    ('array_api_compat', '1.4.1', {
+        'checksums': ['053103b7c0ba73626bff7380abf27a29dc80de144394137bc7455b7eba23d8c0'],
+    }),
+    ('natsort', '8.4.0', {
+        'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
+    }),
+    (name, version, {
+        'checksums': ['16ada7ed7d38552ce56d8e8b2348e18a5fc81294ce8a7ea282acf30dc42cd6c2'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/natsort'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["natsort --help"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/Compass/Compass-2024.04-foss-2022b.eb

@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'Compass'
+version = '2024.04'
+
+homepage = 'https://github.com/YosefLab/Compass'
+description = """In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes."""
+local_commit = "7664cb0"
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('tqdm', '4.64.1'),
+    ('python-libsbml', '5.20.2'),
+    ('scikit-learn', '1.2.1'),
+    ('python-igraph', '0.10.6'),
+    ('leidenalg', '0.10.1'),
+    ('anndata', '0.10.6'),
+    # ('CPLEX', '22.1.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('compass', version, {
+        # delete dependecy python-igraph - pip check failing
+        'preinstallopts': "sed -i '27d' setup.py && ",
+        'source_urls': ['https://github.com/YosefLab/Compass/archive/'],
+        'sources': [{
+            'download_filename': '%s.tar.gz' % local_commit,
+            'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit,
+        }],
+        'checksums': ['87529c5fae108fa2a8e3e35438d3b25874faa78af670a2349228c76fa0843376'],
+    }),
+]
+
+# sanity_check_commands = ["python -c 'import igraph'", "compass -h", "python -c 'import cplex'"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2022b.eb

@@ -0,0 +1,44 @@
+# This is a contribution from SIB Swiss Institute of Bioinformatics
+# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it
+# Authors: Sebastien Moretti <[email protected]>
+# Update: PavelTománek (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'python-libsbml'
+version = '5.20.2'
+
+homepage = 'https://sbml.org/'
+description = """LibSBML Python API."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+    ('make', '4.4.1'),
+    ('Check', '0.15.2'),
+    ('SWIG', '4.1.1'),
+    ('expat', '2.4.9'),
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.2.12'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('libxml2', '2.10.3'),
+    ('libxslt', '1.1.37'),
+]
+
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'modulename': 'libsbml',
+        'checksums': ['0af5cbff68c9b52bac4bd7bb261f93a60832dc8cb31dafc90d3aff51467935b7'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'