{bio}[foss/2022a,gompi/2022a,GCCcore/11.3.0] Model-Angelo v1.0.11 PyHMMER 0.10.4 Cython/3.0.5 /w CUDA 11.7.0

easybuild/easyconfigs/c/Cython/Cython-3.0.5-GCCcore-11.3.0.eb

@@ -0,0 +1,38 @@
+easyblock = 'PythonPackage'
+
+name = 'Cython'
+version = '3.0.5'
+
+homepage = 'https://cython.org/'
+description = """
+Cython is an optimising static compiler for both the Python programming
+language and the extended Cython programming language (based on Pyrex).
+"""
+docurls = [
+    'https://cython.org/#documentation',
+    'https://github.com/cython/cython',
+]
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [('Python', '3.10.4')]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['39318348db488a2f24e7c84e08bdc82f2624853c0fea8b475ea0b70b27176492']
+
+sanity_check_paths = {
+    'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    'cython --version',
+]
+
+moduleclass = 'lang'

easybuild/easyconfigs/m/Model-Angelo/Model-Angelo-1.0.11-foss-2022a-CUDA-11.7.0.eb

@@ -0,0 +1,80 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
+easyblock = 'PythonBundle'
+
+name = 'Model-Angelo'
+versionsuffix = '-CUDA-%(cudaver)s'
+version = '1.0.11'
+
+homepage = 'https://github.com/3dem/model-angelo'
+description = """ModelAngelo is an automatic atomic model building program for cryo-EM maps"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    ('pkg-config', '0.29.2'),
+    ('cppy', '1.2.1'),
+
+]
+
+dependencies = [
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('tqdm', '4.64.0'),
+    ('Biopython', '1.79'),
+    ('einops', '0.4.1'),
+    ('mrcfile', '1.4.3'),
+    ('matplotlib', '3.5.2'),
+    ('PyTorch', '1.12.0', versionsuffix),
+    ('PyHMMER', '0.10.4'),
+    ('Model-Angelo_data', '1.0.9', '', SYSTEM)
+]
+
+use_pip = True
+
+github_account = '3dem'
+
+exts_list = [
+    ('loguru', '0.7.2', {
+        'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'],
+    }),
+    ('fair-esm', '2.0.0', {
+        'modulename': 'esm',
+        'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'],
+    }),
+    (name, version, {
+        'modulename': 'model_angelo',
+        'patches': [
+            'Model-Angelo-1.0.9_relax_requirements.patch',
+            'Model-Angelo-1.0.9_add_init_py.patch',
+            'Model-Angelo-1.0.9_multi_torch_home.patch',
+        ],
+        'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': [
+            {'v1.0.11.tar.gz': '46daba54fb42e75bfb9d845dcf9cc43a6a9bc0d5825d325f46612b772679f57a'},
+            {'Model-Angelo-1.0.9_relax_requirements.patch':
+             '570217999537eb55f5e55bb842a60f58d00850eaace40e5726e2ac058d003986'},
+            {'Model-Angelo-1.0.9_add_init_py.patch':
+             '7d3144ddac92d5800d9a6993bf50a3850627bc836ad01917be531fdd690b72d3'},
+            {'Model-Angelo-1.0.9_multi_torch_home.patch':
+             '950d32ca50f14d04cb7f9cc0c384c1a55979cf88ae7ce5b855bef90a935ce13d'},
+        ],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = [
+    "model_angelo --help",
+]
+
+sanity_check_paths = {
+    'files': [
+        'lib/python%(pyshortver)s/site-packages/model_angelo/utils/stereo_chemical_props.txt'
+    ],
+
+    'dirs': ['lib/python%(pyshortver)s/site-packages/model_angelo']
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/m/Model-Angelo/Model-Angelo-1.0.9_add_init_py.patch

@@ -0,0 +1,33 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
+# add missing __init__.py files in apps, c_alpha, data, gnn, models, and utils
+# in order to allow setup.py.find_packages() to find and install subdirectories
+diff -ruN model-angelo-1.0.9/model_angelo/apps/__init__.py model-angelo-1.0.9_add_init_py/model_angelo/apps/__init__.py
+--- model-angelo-1.0.9/model_angelo/apps/__init__.py	2023-10-27 16:42:58.000000000 +0200
++++ model-angelo-1.0.9_add_init_py/model_angelo/apps/__init__.py	2023-11-06 11:06:16.212950502 +0100
+@@ -0,0 +1 @@
++#
+diff -ruN model-angelo-1.0.9/model_angelo/c_alpha/__init__.py model-angelo-1.0.9_add_init_py/model_angelo/c_alpha/__init__.py
+--- model-angelo-1.0.9/model_angelo/c_alpha/__init__.py	1970-01-01 01:00:00.000000000 +0100
++++ model-angelo-1.0.9_add_init_py/model_angelo/c_alpha/__init__.py	2023-11-06 11:06:16.212950502 +0100
+@@ -0,0 +1 @@
++#
+diff -ruN model-angelo-1.0.9/model_angelo/data/__init__.py model-angelo-1.0.9_add_init_py/model_angelo/data/__init__.py
+--- model-angelo-1.0.9/model_angelo/data/__init__.py	1970-01-01 01:00:00.000000000 +0100
++++ model-angelo-1.0.9_add_init_py/model_angelo/data/__init__.py	2023-11-06 11:06:16.212950502 +0100
+@@ -0,0 +1 @@
++#
+diff -ruN model-angelo-1.0.9/model_angelo/gnn/__init__.py model-angelo-1.0.9_add_init_py/model_angelo/gnn/__init__.py
+--- model-angelo-1.0.9/model_angelo/gnn/__init__.py	1970-01-01 01:00:00.000000000 +0100
++++ model-angelo-1.0.9_add_init_py/model_angelo/gnn/__init__.py	2023-11-06 11:06:16.212950502 +0100
+@@ -0,0 +1 @@
++#
+diff -ruN model-angelo-1.0.9/model_angelo/models/__init__.py model-angelo-1.0.9_add_init_py/model_angelo/models/__init__.py
+--- model-angelo-1.0.9/model_angelo/models/__init__.py	1970-01-01 01:00:00.000000000 +0100
++++ model-angelo-1.0.9_add_init_py/model_angelo/models/__init__.py	2023-11-06 11:06:16.212950502 +0100
+@@ -0,0 +1 @@
++#
+diff -ruN model-angelo-1.0.9/model_angelo/utils/__init__.py model-angelo-1.0.9_add_init_py/model_angelo/utils/__init__.py
+--- model-angelo-1.0.9/model_angelo/utils/__init__.py	1970-01-01 01:00:00.000000000 +0100
++++ model-angelo-1.0.9_add_init_py/model_angelo/utils/__init__.py	2023-11-06 11:10:29.338107389 +0100
+@@ -0,0 +1 @@
++#

easybuild/easyconfigs/m/Model-Angelo/Model-Angelo-1.0.9_multi_torch_home.patch

@@ -0,0 +1,68 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
+# allow to use TORCH_HOME with modextravars.
+# Automatic download of models and language is disabled for multi TORCH_HOME.
+diff -ru model-angelo-1.0.9/model_angelo/utils/misc_utils.py model-angelo-1.0.9_multi_torch_home/model_angelo/utils/misc_utils.py
+--- model-angelo-1.0.9/model_angelo/utils/misc_utils.py	2023-10-27 16:42:58.000000000 +0200
++++ model-angelo-1.0.9_multi_torch_home/model_angelo/utils/misc_utils.py	2023-11-17 18:58:36.581076278 +0100
+@@ -116,10 +116,17 @@
+     warnings.filterwarnings("ignore", ".*with given element none.*")
+     warnings.filterwarnings("ignore", ".*invalid value encountered in true\_divide.*")
+
+-
+ def get_esm_model(esm_model_name):
+     import esm
+     import torch
++    is_torch_home_multi=False if os.getenv('TORCH_HOME')==None else len(os.getenv('TORCH_HOME').split(':'))>1
++    if is_torch_home_multi:
++        for tmp_torch_home in os.getenv('TORCH_HOME').split(':'):
++            tmp_dst = os.path.join(tmp_torch_home, 'hub', 'checkpoints', esm_model_name + ".pt")
++            if os.path.isfile(tmp_dst): 
++                model = esm.pretrained.load_model_and_alphabet_local(tmp_dst)
++                return model
++        assert  False , "None of the paths defined in $TORCH_HOME contains %s" % esm_model_name
+     try:
+         model = esm.pretrained.load_model_and_alphabet_hub(esm_model_name)
+     except:
+diff -ru model-angelo-1.0.9/model_angelo/utils/torch_utils.py model-angelo-1.0.9_multi_torch_home/model_angelo/utils/torch_utils.py
+--- model-angelo-1.0.9/model_angelo/utils/torch_utils.py	2023-10-27 16:42:58.000000000 +0200
++++ model-angelo-1.0.9_multi_torch_home/model_angelo/utils/torch_utils.py	2023-11-14 18:35:39.669951044 +0100
+@@ -446,7 +446,17 @@
+     dest = os.path.join(
+         torch.hub.get_dir(), "checkpoints", "model_angelo_v1.0", bundle_name
+     )
+-    if os.path.isfile(os.path.join(dest, "success.txt")):
++    is_torch_home_multi=False if os.getenv('TORCH_HOME')==None else len(os.getenv('TORCH_HOME').split(':'))>1
++    if (is_torch_home_multi):
++        torch_homes=os.getenv('TORCH_HOME').split(':')
++        for torch_home in torch_homes:
++            dest = os.path.join(
++                torch_home, "hub", "checkpoints", "model_angelo_v1.0", bundle_name
++            )
++            if os.path.isfile(os.path.join(dest, "success.txt")):
++                return dest
++        assert False, "Model ownload disabled, because multiple paths defined in $TORCH_HOME. %s" % dest
++    elif os.path.isfile(os.path.join(dest, "success.txt")):
+         return dest
+
+     print(f"Setting up bundle with name: {bundle_name} for the first time.")
+@@ -503,6 +513,20 @@
+
+
+ def download_and_install_esm_model(esm_model_name: str) -> str:
++    is_torch_home_multi=False if os.getenv('TORCH_HOME')==None else len(os.getenv('TORCH_HOME').split(':'))>1
++    if is_torch_home_multi:
++        torch_homes = os.getenv('TORCH_HOME').split(':')
++        for torch_home in torch_homes:
++            dest_model = os.path.join(
++                torch_home, "checkpoints", esm_model_name + ".pt"
++            )
++            dest_regr = os.path.join(
++                torch_home, "checkpoints", esm_model_name + "-contact-regression.pt"
++            )
++            if os.path.isfile(dest_model) and os.path.isfile(dest_regr):
++                return dest_model    
++        assert is_torch_home_multi==False, 'Language model download disabled, because multiple paths are set in $TORCH_HOME'
++        
+     permissions = (
+         stat.S_IROTH
+         | stat.S_IXOTH

easybuild/easyconfigs/m/Model-Angelo/Model-Angelo-1.0.9_relax_requirements.patch

@@ -0,0 +1,14 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
+# allow to use Biopython/1.79-foss-2022a
+diff -ru model-angelo-1.0.9/setup.py model-angelo-1.0.9_relax_requirements/setup.py
+--- model-angelo-1.0.9/setup.py	2023-10-27 16:42:58.000000000 +0200
++++ model-angelo-1.0.9_relax_requirements/setup.py	2023-11-06 10:12:57.641982769 +0100
+@@ -28,7 +28,7 @@
+     install_requires=[
+         "tqdm",
+         "scipy",
+-        "biopython>=1.81",
++        "biopython>=1.79",
+         "einops",
+         "matplotlib",
+         "mrcfile",

easybuild/easyconfigs/m/Model-Angelo_data/Model-Angelo_data-1.0.9.eb

@@ -0,0 +1,108 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
+easyblock = 'Binary'
+
+name = 'Model-Angelo_data'
+version = '1.0.9'
+
+homepage = 'https://zenodo.org/search?q=7733060'
+description = """A Graph Neural Network Approach to Automated Model Building in Cryo-EM Maps.
+Automated model building and protein identification in cryo-EM maps."""
+
+toolchain = SYSTEM
+
+_prepare = ''
+#  Uncomment and adapt to store data (10GB) elsewhere:
+# _common_data = '/easybuild/data'
+# _prepare = 'mkdir -p  %s/%%(name)s/%%(version)s/torch_home &&' % _common_data
+# _prepare += 'ln -s %s/%%(name)s/%%(version)s/torch_home %%(installdir)s/torch_home &&' % _common_data
+
+buildininstalldir = True
+
+_models = [
+    'original',
+    'original_no_seq',
+    'small_gpu',
+    'nucleotides',
+    'nucleotides_no_seq'
+]
+
+_torch_home = 'torch_home/'
+_checkpoints_rel = '%s/hub/checkpoints' % _torch_home
+_checkpoints = '%%(installdir)s/%s' % _checkpoints_rel
+
+
+source_urls = [
+    'https://dl.fbaipublicfiles.com/fair-esm/models',
+    'https://dl.fbaipublicfiles.com/fair-esm/regression',
+    'https://zenodo.org/records/7733060/files/',
+    'https://zenodo.org/records/7942241/files/',
+]
+sources = [
+    {
+        'filename': 'esm1b_t33_650M_UR50S.pt',
+        'extract_cmd':
+            _prepare +
+            'mkdir -p %s/model_angelo && ' % _checkpoints +
+            'cp -n %%s %s ' % _checkpoints,
+    },
+    {
+        'filename': 'esm1b_t33_650M_UR50S-contact-regression.pt',
+        'extract_cmd': 'cp -n %%s %s ' % _checkpoints,
+    },
+    {
+        'filename':  'original-7733060.zip',
+        'download_filename': 'original.zip',
+        'extract_cmd': 'unzip -n %%s -d %s/model_angelo_v1.0/ ' % _checkpoints
+    },
+    {
+        'filename':  'original_no_seq-7733060.zip',
+        'download_filename': 'original_no_seq.zip',
+        'extract_cmd': 'unzip -n %%s -d %s/model_angelo_v1.0/ ' % _checkpoints
+    },
+    {
+        'filename':  'small_gpu-7733060.zip',
+        'download_filename': 'small_gpu.zip',
+        'extract_cmd': 'unzip -n %%s -d %s/model_angelo_v1.0/ ' % _checkpoints
+    },
+    {
+        'filename':  'nucleotides-7942241.zip',
+        'download_filename': 'nucleotides.zip',
+        'extract_cmd': 'unzip -n %%s -d %s/model_angelo_v1.0/ ' % _checkpoints
+    },
+    {
+        'filename':  'nucleotides_no_seq-7942241.zip',
+        'download_filename': 'nucleotides_no_seq.zip',
+        'extract_cmd': 'unzip -n %%s -d %s/model_angelo_v1.0/ ' % _checkpoints
+    },
+]
+checksums = [
+    {'esm1b_t33_650M_UR50S.pt': '0569754efaff7dcb7e068c27367bc73f10afb4b450ea30aac30d9bc60783a8b1'},
+    {'esm1b_t33_650M_UR50S-contact-regression.pt': '77193a8814f0db0b36a03aebb1a311adc6b4745f463c04839defc15407bbb28a'},
+    {'original-7733060.zip': '55bda1751045030f6ed70af55670819f9ada78055b042b9370080df881b6a5bd'},
+    {'original_no_seq-7733060.zip': '2e66c7748a446b7c7845e7ff60a2b4e515853ba2093062407cff00ce38550a42'},
+    {'small_gpu-7733060.zip': '1c6d69cb568e81661aad2b10bc1197e22fa3ea91271480c0befe89ffaf314948'},
+    {'nucleotides-7942241.zip': 'f1b1d22f563977ac54c7366038c48a8ad37ca2f8870879221149d454cb051041'},
+    {'nucleotides_no_seq-7942241.zip': '3b75de921440dd6891a6c5ea129fafe86e72fd043393f821157e3eda93d685f8'},
+]
+
+skipsteps = ['configure', 'build', 'test']
+extract_sources = True
+
+_success = [
+    'echo Sucessfully downloaded model>%s/model_angelo_v1.0/%s/success.txt'
+    % (_checkpoints, x) for x in _models
+]
+
+install_cmd = '%s ' % '&&'.join(_success)
+
+modextrapaths = {'TORCH_HOME': _torch_home}
+
+sanity_check_paths = {
+    'files': [
+        '%s/esm1b_t33_650M_UR50S.pt' % _checkpoints,
+        '%s/esm1b_t33_650M_UR50S-contact-regression.pt' % _checkpoints_rel,
+    ],
+    'dirs': ['%s/model_angelo_v1.0/%s' % (_checkpoints, m) for m in _models]
+}
+
+moduleclass = 'data'

easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.4-gompi-2022a.eb

@@ -0,0 +1,45 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
+easyblock = 'PythonBundle'
+
+name = 'PyHMMER'
+version = '0.10.4'
+
+homepage = 'https://github.com/althonos/pyhmmer'
+description = """
+HMMER is a biological sequence analysis tool that uses profile hidden Markov    
+models to search for sequence homologs. HMMER3 is developed and maintained by   
+the Eddy/Rivas Laboratory at Harvard University.
+
+pyhmmer is a Python package, implemented using the Cython language, that        
+provides bindings to HMMER3. It directly interacts with the HMMER internals,    
+which has the following advantages over CLI wrappers (like hmmer-py)"""
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+toolchainopts = {}  # toolchain options, e.g. opt, pic, usempi, optarch, ...
+
+
+builddependencies = [
+    # Cython 0.29.28 does not work
+    ('Cython', '3.0.5'),
+]
+dependencies = [
+    ('Python', '3.10.4'),
+    ('HMMER', '3.3.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('pyhmmer', version, {
+        'checksums': ['08bc02aadf0f113df2b2912478bb02be9daf5d322df9c72bcd07fa01fe53a87b'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
+}
+
+sanity_pip_check = True
+
+moduleclass = 'bio'