{bio}[foss/2023a] Model-Angelo v1.0.14 w/ CUDA 12.1.1

easybuild/easyconfigs/m/Model-Angelo/Model-Angelo-1.0.14-foss-2023a-CUDA-12.1.1.eb

@@ -0,0 +1,73 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2025/05
+easyblock = 'PythonBundle'
+
+name = 'Model-Angelo'
+versionsuffix = '-CUDA-%(cudaver)s'
+version = '1.0.14'
+
+homepage = 'https://github.com/3dem/model-angelo'
+description = "ModelAngelo is an automatic atomic model building program for cryo-EM maps."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('pkgconf', '1.9.5'),
+    ('cppy', '1.2.1'),
+
+]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),  # violates req. numpy==1.21.*
+    ('tqdm', '4.66.1'),
+    ('Biopython', '1.83'),
+    ('einops', '0.7.0'),
+    ('mrcfile', '1.5.0'),
+    ('matplotlib', '3.7.2'),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('PyHMMER', '0.10.6'),  # violates req. 0.7.1
+    ('ESM-2', '2.0.0', versionsuffix),  # violates req. 1.0.3
+    ('Model-Angelo_data', '1.0.0', '', SYSTEM)
+]
+
+github_account = '3dem'
+
+exts_list = [
+    ('loguru', '0.7.2', {
+        'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'],
+    }),
+    (name, version, {
+        'modulename': 'model_angelo',
+        'patches': [
+            'Model-Angelo-1.0.9_add_init_py.patch',
+            'Model-Angelo-1.0.9_multi_torch_home.patch',
+            'Model-Angelo-1.0.14_relax_requirements.patch',
+        ],
+        'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': [
+            {'v1.0.14.tar.gz': 'ebeec3de2755c394f8d6d74ce96910c848b2513ea4279de29255b8aceacc94a8'},
+            {'Model-Angelo-1.0.9_add_init_py.patch':
+             '7d3144ddac92d5800d9a6993bf50a3850627bc836ad01917be531fdd690b72d3'},
+            {'Model-Angelo-1.0.9_multi_torch_home.patch':
+             '950d32ca50f14d04cb7f9cc0c384c1a55979cf88ae7ce5b855bef90a935ce13d'},
+            {'Model-Angelo-1.0.14_relax_requirements.patch':
+             'f85362268248b959d4ae65e89ec625d031e17f93f1607e1fbd35d52ec2fc3a5b'},
+        ],
+    }),
+]
+
+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-1.0.14_relax_requirements.patch

@@ -0,0 +1,16 @@
+diff -ru model-angelo-1.0.14/setup.py model-angelo-1.0.14_requirements/setup.py
+--- model-angelo-1.0.14/setup.py	2025-05-08 13:15:47.000000000 +0200
++++ model-angelo-1.0.14_requirements/setup.py	2025-05-23 11:16:34.285077409 +0200
+@@ -33,9 +33,9 @@
+         "matplotlib",
+         "mrcfile",
+         "pandas",
+-        "fair-esm==1.0.3",
+-        "pyhmmer==0.7.1",
++        "fair-esm<=2.0.0",
++        "pyhmmer<=1.10.15",
+         "loguru",
+-        "numpy<2.0,
++        "numpy<=1.25.1",
+     ],
+ )

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_data/Model-Angelo_data-1.0.0.eb

@@ -0,0 +1,108 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/10
+easyblock = 'Binary'
+
+name = 'Model-Angelo_data'
+version = '1.0.0'
+
+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'