{bio}[foss/2021b] AlphaFold v2.3.0 w/ Python 3.9.6 + CUDA 11.4.1

easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb

@@ -0,0 +1,167 @@
+easyblock = 'PythonBundle'
+
+name = 'AlphaFold'
+version = '2.3.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://deepmind.com/research/case-studies/alphafold'
+description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known"
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+builddependencies = [
+    # required for installing dm-tree
+    ('Bazel', '3.7.2'),
+    ('CMake', '3.22.1'),
+]
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('CUDA', '11.4.1', '', SYSTEM),
+    ('SciPy-bundle', '2021.10'),
+    ('PyYAML', '5.4.1'),
+    ('TensorFlow', '2.7.1', versionsuffix),
+    ('Biopython', '1.79'),
+    ('HH-suite', '3.3.0'),
+    ('HMMER', '3.3.2'),
+    ('Kalign', '3.3.2'),
+    ('jax', '0.3.23', versionsuffix),  # also provides absl-py
+    ('UCX-CUDA', '1.11.2', versionsuffix),
+    ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM),
+    ('NCCL', '2.10.3', versionsuffix),
+    ('OpenMM', '7.5.1', '-DeepMind-patch'),
+]
+
+# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common,
+# see docker/Dockerfile in AlphaFold repository
+local_scp_commit = '7102c6'
+
+components = [
+    (name, version, {
+        'easyblock': 'PythonPackage',
+        'source_urls': [
+            'https://github.com/deepmind/alphafold/archive/refs/tags/',
+            'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit,
+        ],
+        'sources': [
+            {
+                'download_filename': 'v%(version)s.tar.gz',
+                'filename': SOURCE_TAR_GZ,
+            },
+            {
+                'download_filename': 'stereo_chemical_props.txt',
+                'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit,
+                'extract_cmd': "cp %s .",
+            },
+        ],
+        'patches': [
+            'AlphaFold-2.0.0_fix-packages.patch',
+            'AlphaFold-2.3.0_data-dep-paths.patch',
+            'AlphaFold-2.0.0_n-cpu.patch',
+            'AlphaFold-2.1.0_fix-scp-path.patch',
+            'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
+        ],
+        'checksums': [
+            '52055a0b4bf194ae0e1960e6391e501490f82274c975e01c1ff0e353a1cd59d9',  # v2.3.0.tar.gz
+            '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451',  # stereo_chemical_props-7102c6.txt
+            '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
+            '5cff3fc7104e020ef546d23cb4fb1b8d6517562783f055cc55fc65fe2b0248d0',  # AlphaFold-2.3.0_data-dep-paths.patch
+            'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04',  # AlphaFold-2.0.0_n-cpu.patch
+            '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f',  # AlphaFold-2.1.0_fix-scp-path.patch
+            '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac',  # AlphaFold-2.0.1_setup_rm_tfcpu.patch
+
+        ],
+        'start_dir': 'alphafold-%(version)s',
+        'use_pip': True,
+    }),
+]
+
+use_pip = True
+
+exts_list = [
+    ('PDBFixer', '1.7', {
+        'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'],
+    }),
+    ('toolz', '0.11.2', {
+        'checksums': ['6b312d5e15138552f1bda8a4e66c30e236c831b612b2bf0005f8a1df10a4bc33'],
+    }),
+    ('chex', '0.1.5', {
+        'checksums': ['686858320f8f220c82a6c7eeb54dcdcaa4f3d7f66690dacd13a24baa1ee8299e'],
+    }),
+    ('tabulate', '0.8.10', {
+        'checksums': ['6c57f3f3dd7ac2782770155f3adb2db0b1a269637e42f27599925e64b114f519'],
+    }),
+    ('jmp', '0.0.2', {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'checksums': ['fdb5cec0d10aab4116c2770f24b2adf4f503fcfbb96ce8ef583e1879bdbf1b9b'],
+    }),
+    ('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'],
+    }),
+    ('dm-tree', '0.1.7', {
+        'modulename': 'tree',
+        'checksums': ['30fec8aca5b92823c0e796a2f33b875b4dccd470b57e91e6c542405c5f77fd2a'],
+    }),
+    ('websocket-client', '1.3.3', {
+        'modulename': 'websocket',
+        'checksums': ['d58c5f284d6a9bf8379dab423259fe8f85b70d5fa5d2916d5791a84594b122b1'],
+    }),
+    ('docker', '5.0.3', {
+        'checksums': ['d916a26b62970e7c2f554110ed6af04c7ccff8e9f81ad17d0d40c75637e227fb'],
+    }),
+    ('immutabledict', '2.2.1', {
+        'checksums': ['1ddb0edf1bb6c70d0197eb90ce1fe2b2d58502334f5fdfde72d7c633d723ec3a'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml_collections', '0.1.1', {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+    }),
+]
+
+postinstallcmds = [
+    "mkdir -p %(installdir)s/bin",
+    # run_alphafold.py script is missing a shebang...
+    "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py",
+    "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py",
+    "chmod a+x %(installdir)s/bin/run_alphafold*.py",
+    "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold",
+    "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/",
+    "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit,
+    # run tests for run_alphafold.py script;
+    # shouldn't do this in sanity check to avoid breaking use of --module-only
+    "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH "
+    "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py",
+]
+
+sanity_check_paths = {
+    'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'],
+}
+
+sanity_check_commands = [
+    "pdbfixer --help",
+    "python -m simtk.testInstallation",
+    "python -c 'import alphafold'",
+    "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'",
+]
+
+sanity_pip_check = True
+
+# these allow to make predictions on proteins that would typically be too long to fit into GPU memory;
+# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py
+modextravars = {
+    'TF_FORCE_UNIFIED_MEMORY': '1',
+    'XLA_PYTHON_CLIENT_MEM_FRACTION': '3',
+    # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs',  # please adapt
+    'OPENMM_RELAX': 'CUDA'  # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0_data-dep-paths.patch

@@ -0,0 +1,136 @@
+pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data
+(see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py);
+pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild
+author: Kenneth Hoste (HPC-UGent)
+update 2.0.1 -> 2.1.0/2.1.2/2.3.0: Thomas Hoffmann (EMBL);
+diff -ru alphafold-2.3.0/run_alphafold.py alphafold-2.3.0_data-dep-paths/run_alphafold.py
+--- alphafold-2.3.0/run_alphafold.py	2022-12-11 20:36:44.000000000 +0100
++++ alphafold-2.3.0_data-dep-paths/run_alphafold.py	2022-12-13 17:36:37.258678676 +0100
+@@ -40,6 +40,46 @@
+ import numpy as np
+
+ # Internal import (7716).
++use_reduced_dbs = any("--db_preset=reduced_dbs" in s for s in sys.argv[1:])
++use_monomer_preset = not any("--model_preset=multimer" in s for s in sys.argv[1:])
++
++data_dir = os.getenv('ALPHAFOLD_DATA_DIR')
++use_gpu_relax = os.getenv('OPENMM_RELAX')=='CUDA'
++
++if data_dir:
++    mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters_2022_05.fa')
++    uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta')
++    template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files')
++    obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat')
++    if use_monomer_preset:
++        pdb_seqres_database_path = None
++        uniprot_database_path = None
++        pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70')
++    else:
++        pdb_seqres_database_path = os.path.join(data_dir, 'pdb_seqres', 'pdb_seqres.txt')
++        uniprot_database_path = os.path.join(data_dir, 'uniprot', 'uniprot.fasta')
++        pdb70_database_path = None
++    if use_reduced_dbs:
++        small_bfd_database_path =  os.path.join(data_dir, 'small_bfd','bfd-first_non_consensus_sequences.fasta')
++        uniref30_database_path = None 
++        bfd_database_path = None 
++    else:
++        small_bfd_database_path = None 
++        bfd_database_path = os.path.join(data_dir, 'bfd', 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt')
++        uniref30_database_path = os.path.join(data_dir, 'uniref30', 'UniRef30_2021_03')
++else:
++    sys.stderr.write("$ALPHAFOLD_DATA_DIR is not defined!")
++    uniref90_database_path = None
++    mgnify_database_path = None
++    bfd_database_path = None
++    uniref30_database_path = None
++    pdb70_database_path = None
++    template_mmcif_dir = None
++    obsolete_pdbs_path = None
++    small_bfd_database_path = None
++    uniprot_database_path = None
++    pdb_seqres_database_path = None 
++    use_gpu_relax = None
+
+ logging.set_verbosity(logging.INFO)
+
+@@ -50,7 +90,7 @@
+     'separated by commas. All FASTA paths must have a unique basename as the '
+     'basename is used to name the output directories for each prediction.')
+
+-flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.')
++flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.')
+ flags.DEFINE_string('output_dir', None, 'Path to a directory that will '
+                     'store the results.')
+ flags.DEFINE_string('jackhmmer_binary_path', shutil.which('jackhmmer'),
+@@ -65,27 +105,27 @@
+                     'Path to the hmmbuild executable.')
+ flags.DEFINE_string('kalign_binary_path', shutil.which('kalign'),
+                     'Path to the Kalign executable.')
+-flags.DEFINE_string('uniref90_database_path', None, 'Path to the Uniref90 '
++flags.DEFINE_string('uniref90_database_path', uniref90_database_path, 'Path to the Uniref90 '
+                     'database for use by JackHMMER.')
+-flags.DEFINE_string('mgnify_database_path', None, 'Path to the MGnify '
++flags.DEFINE_string('mgnify_database_path', mgnify_database_path, 'Path to the MGnify '
+                     'database for use by JackHMMER.')
+-flags.DEFINE_string('bfd_database_path', None, 'Path to the BFD '
++flags.DEFINE_string('bfd_database_path', bfd_database_path, 'Path to the BFD '
+                     'database for use by HHblits.')
+-flags.DEFINE_string('small_bfd_database_path', None, 'Path to the small '
++flags.DEFINE_string('small_bfd_database_path', small_bfd_database_path, 'Path to the small '
+                     'version of BFD used with the "reduced_dbs" preset.')
+-flags.DEFINE_string('uniref30_database_path', None, 'Path to the UniRef30 '
++flags.DEFINE_string('uniref30_database_path', uniref30_database_path, 'Path to the UniRef30 '
+                     'database for use by HHblits.')
+-flags.DEFINE_string('uniprot_database_path', None, 'Path to the Uniprot '
++flags.DEFINE_string('uniprot_database_path', uniprot_database_path, 'Path to the Uniprot '
+                     'database for use by JackHMMer.')
+-flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 '
++flags.DEFINE_string('pdb70_database_path', pdb70_database_path, 'Path to the PDB70 '
+                     'database for use by HHsearch.')
+-flags.DEFINE_string('pdb_seqres_database_path', None, 'Path to the PDB '
++flags.DEFINE_string('pdb_seqres_database_path', pdb_seqres_database_path, 'Path to the PDB '
+                     'seqres database for use by hmmsearch.')
+-flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with '
++flags.DEFINE_string('template_mmcif_dir', template_mmcif_dir, 'Path to a directory with '
+                     'template mmCIF structures, each named <pdb_id>.cif')
+ flags.DEFINE_string('max_template_date', None, 'Maximum template release date '
+                     'to consider. Important if folding historical test sets.')
+-flags.DEFINE_string('obsolete_pdbs_path', None, 'Path to file containing a '
++flags.DEFINE_string('obsolete_pdbs_path', obsolete_pdbs_path, 'Path to file containing a '
+                     'mapping from obsolete PDB IDs to the PDB IDs of their '
+                     'replacements.')
+ flags.DEFINE_enum('db_preset', 'full_dbs',
+@@ -124,7 +164,7 @@
+                      'result in predictions with distracting stereochemical '
+                      'violations but might help in case you are having issues '
+                      'with the relaxation stage.')
+-flags.DEFINE_boolean('use_gpu_relax', None, 'Whether to relax on GPU. '
++flags.DEFINE_boolean('use_gpu_relax', use_gpu_relax, 'Whether to relax on GPU. '
+                      'Relax on GPU can be much faster than CPU, so it is '
+                      'recommended to enable if possible. GPUs must be available'
+                      ' if this setting is enabled.')
+@@ -296,6 +336,10 @@
+                        'sure it is installed on your system.')
+
+   use_small_bfd = FLAGS.db_preset == 'reduced_dbs'
++  if use_small_bfd and data_dir:
++    bfd_database_path = None
++    uniref30_database_path = None
++  
+   _check_flag('small_bfd_database_path', 'db_preset',
+               should_be_set=use_small_bfd)
+   _check_flag('bfd_database_path', 'db_preset',
+@@ -420,13 +464,7 @@
+   flags.mark_flags_as_required([
+       'fasta_paths',
+       'output_dir',
+-      'data_dir',
+-      'uniref90_database_path',
+-      'mgnify_database_path',
+-      'template_mmcif_dir',
+       'max_template_date',
+-      'obsolete_pdbs_path',
+-      'use_gpu_relax',
+   ])
+
+   app.run(main)