diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch new file mode 100644 index 000000000000..34994664f805 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch @@ -0,0 +1,13 @@ +fix import of protein_letters_3to1 from Biopython +author: Kenneth Hoste (HPC-UGent) +--- AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py.orig 2024-06-05 09:30:16.114746286 +0200 ++++ AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py 2024-06-05 09:30:35.242665615 +0200 +@@ -4,7 +4,7 @@ + from alphafold.data.mmcif_parsing import parse + from alphafold.common.residue_constants import residue_atoms, atom_types + from Bio.PDB import NeighborSearch, PDBIO, MMCIFIO +-from Bio.PDB.Polypeptide import protein_letters_3to1 ++from Bio.Data.SCOPData import protein_letters_3to1 + from Bio import SeqIO + from colabfold.batch import convert_pdb_to_mmcif + from Bio.PDB import Structure, Model, Chain, Residue diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb new file mode 100644 index 000000000000..f410c438e236 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb @@ -0,0 +1,104 @@ +# created by Denis Kristak (Inuits) +easyblock = 'PythonBundle' + +name = 'AlphaPulldown' +version = '2.0.0b4' + +homepage = 'https://github.com/KosinskiLab/AlphaPulldown' +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('OpenMM', '8.0.0'), + ('Kalign', '3.3.5'), + ('PyYAML', '6.0'), + ('jax', '0.3.25'), # also provides absl-py + ('Biopython', '1.79'), + ('h5py', '3.7.0'), + ('IPython', '8.5.0'), + ('JupyterLab', '3.5.0'), + ('matplotlib', '3.5.2'), + ('TensorFlow', '2.11.0'), + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), + ('dm-tree', '0.1.8'), + ('py3Dmol', '2.0.1.post1'), + ('HMMER', '3.3.2'), + ('HH-suite', '3.3.0'), + ('Uni-Core', '0.0.3'), +] + +use_pip = True + +exts_list = [ + ('importlib-resources', '5.13.0', { + 'modulename': 'importlib_resources', + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['82d5c6cca930697dbbd86c93333bb2c2e72861d4789a11c2662b933e5ad2b528'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('ihm', '1.3', { + 'checksums': ['09f69809fd81509cc26b60253c55b02ce79fc01fc8f4a068bca2953a7dfd33be'], + }), + ('modelcif', '1.0', { + 'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'], + }), + (name, version, { + 'sources': [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/KosinskiLab', + 'repo_name': 'AlphaPulldown', + 'tag': version, + 'recursive': True, + }, + }], + 'patches': ['AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch'], + 'checksums': [ + None, + 'd41247cd12f6ef8579adbc893f6c1af5fba051167ee838449974365f4bdccf06', + ], + # remove strict version requirements for Python dependencies + 'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ", + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], +} + +sanity_check_commands = [ + "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'", + "convert_to_modelcif.py --help | grep 'turn it into a ModelCIF'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb new file mode 100644 index 000000000000..d82f94349bc9 --- /dev/null +++ b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'Uni-Core' +version = '0.0.3' + +homepage = 'https://github.com/dptech-corp/Uni-Core' +description = "An efficient distributed PyTorch framework" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('jax', '0.3.25'), # provides absl-py + ('tensorboardX', '2.5.1'), + ('tqdm', '4.64.0'), + ('wandb', '0.13.4'), +] + +use_pip = True + +local_preinstallopts = "sed -i -e 's/DISABLE_CUDA_EXTENSION = False/DISABLE_CUDA_EXTENSION = True/g' " +local_preinstallopts += "-e 's/torch>=[0-9.]*/torch/g' setup.py && " + +exts_list = [ + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), + ('huggingface-hub', '0.17.3', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'], + }), + ('tokenizers', '0.19.1', { + 'sources': ['tokenizers-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl'], + 'checksums': ['8b01afb7193d47439f091cd8f070a1ced347ad0f9144952a30a41836902fe09e'], + }), + (name, version, { + 'source_urls': ['https://github.com/dptech-corp/Uni-Core/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['e7a1e938d7d340d7aa483a05ed5ecf715bfa22f5f32a92e46d096da5b9a08043'], + 'preinstallopts': local_preinstallopts, + 'modulename': 'unicore', + }), +] + +sanity_pip_check = True + +moduleclass = 'ai'