diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..e1dd253f812 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,121 @@ +# created by Denis Kristak (Inuits) +# update: Thomas Hoffmann, EMBL +easyblock = 'PythonBundle' + +name = 'AlphaPulldown' +version = '2.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +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': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('OpenMM', '8.0.0', versionsuffix), + ('Kalign', '3.4.0'), + ('PyYAML', '6.0'), + ('jax', '0.4.25', versionsuffix), # also provides absl-py + ('Biopython', '1.83'), + ('h5py', '3.9.0'), + ('IPython', '8.14.0'), + ('matplotlib', '3.7.2'), + # ('TensorFlow', '2.15.1', versionsuffix), + ('TensorFlow', '2.13.0'), # to be consistent with AF2 ? + ('PyTorch', '2.1.2', versionsuffix), + ('tqdm', '4.66.1'), + ('dm-tree', '0.1.8'), + ('py3Dmol', '2.1.0'), + ('HMMER', '3.4'), + ('HH-suite', '3.3.0'), + ('dm-haiku', '0.0.12', versionsuffix), + ('Uni-Core', '0.0.3', versionsuffix), + ('JupyterLab', '4.0.5'), +] +local_commit = 'cc4b0af60518c078305bbe4c584691d1ed9ade31' +use_pip = True + +local_tests = [ + 'custom_db', + 'remove_clashes_low_plddt', + 'modelcif', + 'features_with_templates', + 'post_prediction', + # require pyrosetta, analysis aptainer image, and AlphaFold2 data: + # 'pdb_analyser', + # 'get_good_inter_pae', +] +local_testinstall_PATH = """ PATH=$(echo $PYTHONPATH|awk -F ':' '{print $1}')/../../../bin:$PATH """ +exts_list = [ + ('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'], + }), + ('looseversion', '1.1.2', { + 'checksums': ['94d80bdbd0b6d57c11b886147ba1601f7d1531571621b81933b34537cbe469ad'], + }), + ('mmtf-python', '1.1.3', { + 'modulename': 'mmtf', + 'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'], + }), + ('biopandas', '0.5.1.dev0', { + 'checksums': ['6dc9de631babf8221c1ac60230133717039e08911f15e8ac48498c787022de12'], + }), + ('immutabledict', '4.1.0', { + 'checksums': ['93d100ccd2cd09a1fd3f136b9328c6e59529ba341de8bb499437f6819159fe8a'], + }), + (name, version, { + 'preinstallopts': "sed -i 's/[>=]=.*//g;s/tensorflow-cpu/tensorflow/g' setup.cfg && ", + 'runtest': '%s pytest -s %s ' % (local_testinstall_PATH, " ".join('test/test_%s.py' % x for x in local_tests)), + 'sources': [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/KosinskiLab', + 'repo_name': 'AlphaPulldown', + 'tag': version, 'recursive': True + } + }], + 'testinstall': True, + # This needs to be [None], at least until EB v5 is out + # 'checksums': ['e338195987e003f3caadb06bda0ca56dece87e358738143ea72662f9ad69b1d4'], + 'checksums': [None], + }), +] + +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', + 'lib/python%(pyshortver)s/site-packages/alphafold/common/stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], +} + +sanity_check_commands = [ + "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'", + "create_individual_features.py --helpfull|grep 'Additional allowance for hydrogen bonding'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..24fb0a0d2e2 --- /dev/null +++ b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'Uni-Core' +version = '0.0.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/dptech-corp/Uni-Core' +description = "An efficient distributed PyTorch framework" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('maturin', '1.4.0', '-Rust-1.75.0') +] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), + ('jax', '0.4.25', versionsuffix), # provides absl-py + ('tensorboardX', '2.6.2.2'), + ('tqdm', '4.66.1'), + ('wandb', '0.16.1'), +] + +use_pip = True +local_preinstallopts = "sed -i " +# local_preinstallopts += "-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', '1.5.1', { + 'checksums': ['717c255827d331e02f7242b44051aa06466c90f6d732ecb07b31edfb1e06c67a'], + }), + ('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'], + }), + ('huggingface-hub', '0.24.5', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], + }), + ('tokenizers', '0.20.0', { + 'checksums': ['39d7acc43f564c274085cafcd1dae9d36f332456de1a31970296a6b8da4eac8d'], + }), + (name, version, { + 'modulename': 'unicore', + 'preinstallopts': local_preinstallopts, + 'source_urls': ['https://github.com/dptech-corp/Uni-Core/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['e7a1e938d7d340d7aa483a05ed5ecf715bfa22f5f32a92e46d096da5b9a08043'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai'