From 968e9b1ee34a770b7aca7c67657d195e22cabd81 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 21 Dec 2025 13:34:34 +0100 Subject: [PATCH 1/3] adding easyconfigs: BioEmu-1.2.0-foss-2024a.eb --- .../b/BioEmu/BioEmu-1.2.0-foss-2024a.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioEmu/BioEmu-1.2.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/b/BioEmu/BioEmu-1.2.0-foss-2024a.eb b/easybuild/easyconfigs/b/BioEmu/BioEmu-1.2.0-foss-2024a.eb new file mode 100644 index 00000000000..505f7aebc85 --- /dev/null +++ b/easybuild/easyconfigs/b/BioEmu/BioEmu-1.2.0-foss-2024a.eb @@ -0,0 +1,73 @@ +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'), + ('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, { + # uv only needed for a setup script in bioemu that installs colabfold + 'preinstallopts': "sed -i '/.uv.,/d' pyproject.toml &&", + 'checksums': ['be262f913ab700d43da743f2e8ea171e70b293fcceefbaac5e2b4d5e904fa6cf'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bio', 'bin/typer'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [ + "python -m bioemu.sample --help", +] + +moduleclass = 'bio' From 1cea06afe9dcb1d31ba8f3c8bf2c80e2bfa91f7f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 21 Dec 2025 16:12:05 +0100 Subject: [PATCH 2/3] adding easyconfigs: mygene-3.2.2-foss-2024a.eb --- .../m/mygene/mygene-3.2.2-foss-2024a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2024a.eb diff --git a/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2024a.eb b/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2024a.eb new file mode 100644 index 00000000000..feccccc7bbf --- /dev/null +++ b/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' From 5863f893a0dd8189874b7f0c75fc56e79c2f674c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 1 Mar 2026 11:39:43 +0100 Subject: [PATCH 3/3] add dependency on ColabFold to BioEmu v1.2.0 --- .../b/BioEmu/BioEmu-1.2.0-foss-2024a.eb | 22 ++++++++++++++++--- 1 file changed, 19 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BioEmu/BioEmu-1.2.0-foss-2024a.eb b/easybuild/easyconfigs/b/BioEmu/BioEmu-1.2.0-foss-2024a.eb index 505f7aebc85..d86e9015fc1 100644 --- a/easybuild/easyconfigs/b/BioEmu/BioEmu-1.2.0-foss-2024a.eb +++ b/easybuild/easyconfigs/b/BioEmu/BioEmu-1.2.0-foss-2024a.eb @@ -21,6 +21,7 @@ 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'), @@ -55,19 +56,34 @@ exts_list = [ 'checksums': ['be516bd9fe4dfee562a521d22ffa4b94ee662b9f2a53a4dd52a0a00d93521354'], }), ('bioemu', version, { - # uv only needed for a setup script in bioemu that installs colabfold + '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 &&", - 'checksums': ['be262f913ab700d43da743f2e8ea171e70b293fcceefbaac5e2b4d5e904fa6cf'], }), ] +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/'], + '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'