Merge pull request easybuilders#21204 from ThomasHoffmann77/202408172…

…00306_new_pr_AlphaPulldown200b4

{bio}[foss/2023a] AlphaPulldown v2.0.0 Uni-Core v0.0.3 w/ CUDA v12.1.1

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'

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'