{bio}[foss/2024a] BioEmu v1.2.0

easybuild/easyconfigs/b/BioEmu/BioEmu-1.2.0-foss-2024a.eb

@@ -0,0 +1,89 @@
+easyblock = 'PythonBundle'
+
+name = 'BioEmu'
+version = '1.2.0'
+
+homepage = 'https://github.com/microsoft/bioemu'
+description = """
+Biomolecular Emulator (BioEmu for short) is a model that samples from the
+approximated equilibrium distribution of structures for a protein monomer,
+given its amino acid sequence.
+"""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+builddependencies = [
+    ('PDM', '2.18.2'),
+    ('hatchling', '1.27.0'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('PyTorch-Geometric', '2.6.1'),
+    ('ColabFold', '1.5.5'),
+    ('Biopython', '1.84'),
+    ('dm-tree', '0.1.9'),
+    ('MDTraj', '1.10.3'),
+    ('mygene', '3.2.2'),
+]
+
+exts_list = [
+    ('typer', '0.19.2', {
+        'checksums': ['9ad824308ded0ad06cc716434705f691d4ee0bfd0fb081839d2e426860e7fdca'],
+    }),
+    ('termcolor', '2.5.0', {
+        'checksums': ['998d8d27da6d48442e8e1f016119076b690d962507531df4890fcd2db2ef8a6f'],
+    }),
+    ('fire', '0.7.0', {
+        'checksums': ['961550f07936eaf65ad1dc8360f2b2bf8408fad46abbfa4d2a3794f8d2a95cdf'],
+    }),
+    ('ihm', '1.8', {
+        'checksums': ['6c19813642487a5af3603beb51a1854559e55ccaa8fddd10986c3026a11b948f'],
+    }),
+    ('modelcif', '0.7', {
+        'checksums': ['d6acedb2c0afb7a6964b15aa275926dd8b55c88217ae82279a1667f33f6316de'],
+    }),
+    ('stackprinter', '0.2.12', {
+        'checksums': ['271efc75ebdcc1554e58168ea7779f98066d54a325f57c7dc19f10fa998ef01e'],
+    }),
+    ('gprofiler-official', '1.0.0', {
+        'modulename': 'gprofiler',
+        'checksums': ['5015b47f10fbdcb59c57e342e815c9c07afbe57cd3984154f75b845ddef2445d'],
+    }),
+    ('bio', '1.8.1', {
+        'modulename': False,  # just a 'bio' executable
+        'checksums': ['be516bd9fe4dfee562a521d22ffa4b94ee662b9f2a53a4dd52a0a00d93521354'],
+    }),
+    ('bioemu', version, {
+        'source_urls': ['https://github.com/microsoft/bioemu/archive'],
+        'sources': [{'download_filename': 'v.%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['c9eee5bdaccaf11ad82d99e0f6af06cb1733186ccac7e9dc14ad43e88a472bb3'],
+        # remove uv, needed for a setup script that installs colabfold (we provide it)
+        'preinstallopts': "sed -i '/.uv.,/d' pyproject.toml &&",
+    }),
+]
+
+postinstallcmds = [
+    # copy notebooks to installation directory
+    "cp -r notebooks %(installdir)s/",
+]
+
+sanity_check_paths = {
+    'files': ['bin/bio', 'bin/typer'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/', 'notebooks'],
+}
+
+sanity_check_commands = [
+    "python -m bioemu.sample --help",
+]
+
+modextravars = {
+    'BIOEMU_COLABFOLD_DIR': '$EBROOTCOLABFOLD',
+}
+
+modloadmsg = """
+%(name)s notebooks are located in $EBROOTBIOEMU/notebooks
+"""
+
+moduleclass = 'bio'

easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2024a.eb

@@ -0,0 +1,29 @@
+# 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': '2024a'}
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+]
+
+exts_list = [
+    ('biothings_client', '0.3.1', {
+        'checksums': ['c972bf2e02b6f9cc78f7f2fbc5ef02cc56fe4f8a2adcb8801ec902f4ab7011e6'],
+    }),
+    (name, version, {
+        'checksums': ['e729cabbc28cf5afb221bca1ab637883b375cb1a3e2f067587ec79f71affdaea'],
+    }),
+]
+
+moduleclass = 'bio'