Merge pull request #21791 from PetrKralCZ/20241106144430_new_pr_BindC…

…raft110

{bio}[foss/2023a] BindCraft v1.1.0, PyRosetta v4.release-387, dm-haiku v0.0.13

easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb

@@ -0,0 +1,89 @@
+easyblock = 'Tarball'
+
+name = 'BindCraft'
+version = '1.1.0'
+
+homepage = 'https://github.com/martinpacesa/BindCraft'
+description = """Simple binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta.
+ Select your target and let the script do the rest of the work and finish once you have enough designs to order!"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/martinpacesa/BindCraft/archive/refs/tags/']
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}]
+checksums = ['c682f59501f0bcfbb8289fd066362dcea37ed8553cdff5c794a2baa6d4149ce7']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Biopython', '1.83'),
+    ('Seaborn', '0.13.2'),
+    ('tqdm', '4.66.1'),
+    ('OpenMM', '8.0.0'),
+    ('FFmpeg', '6.0'),
+    ('matplotlib', '3.7.2'),
+    ('PyRosetta', '4.release-387'),
+    ('jax', '0.4.25'),
+    ('dm-haiku', '0.0.13'),
+    ('dm-tree', '0.1.8'),
+    ('ml-collections', '0.1.1'),
+    ('Optax', '0.2.2'),
+    ('py3Dmol', '2.1.0'),
+    ('JupyterLab', '4.0.5'),
+    ('hatchling', '1.18.0'),
+    ('Flax', '0.8.4'),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+}
+exts_list = [
+    ('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'],
+    }),
+    ('jupyter_console', '6.6.3', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'],
+    }),
+    # older version compatible with `jupyterlab-4.0.5`
+    ('notebook', '7.0.8', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['7f421b3fd46a17d91830e724b94e8e9ae922af152ebfd48b1e13ae4a07d8193c'],
+    }),
+    ('jupyter', '1.1.1', {
+        'source_tmpl': SOURCE_WHL,
+        'checksums': ['7a59533c22af65439b24bbe60373a4e95af8f16ac65a6c00820ad378e3f7cc83'],
+    }),
+    ('immutabledict', '4.2.0', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['d728b2c2410d698d95e6200237feb50a695584d20289ad3379a439aa3d90baba'],
+    }),
+    ('colabdesign', '1.1.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['8f556fb575d2bbef79fa1789698d55221f2cc51df38f2cc054f38cb6ecc08e27'],
+    }),
+]
+
+fix_python_shebang_for = ['bindcraft.py']
+
+postinstallcmds = ['chmod a+x %(installdir)s/bindcraft.py']
+
+modextrapaths = {
+    'PATH': '',
+    'PYTHONPATH': ['', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_paths = {
+    'files': ['bindcraft.py'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["bindcraft.py --help"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb

@@ -0,0 +1,34 @@
+easyblock = 'PythonBundle'
+
+name = 'dm-haiku'
+version = '0.0.13'
+
+homepage = 'https://github.com/deepmind/dm-haiku'
+description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural
+network library for TensorFlow."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('jax', '0.4.25'),  # required by jmp, also provides absl-py
+]
+
+use_pip = True
+
+exts_list = [
+    ('jmp', '0.0.4', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['6aa7adbddf2bd574b28c7faf6e81a735eb11f53386447896909c6968dc36807d'],
+    }),
+    ('dm_haiku', version, {
+        'modulename': 'haiku',
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['ee9562c68a059f146ad07f555ca591cb8c11ef751afecc38353863562bd23f43'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb

@@ -0,0 +1,38 @@
+easyblock = 'PythonBundle'
+
+name = 'PyRosetta'
+version = '4.release-387'
+
+homepage = 'https://www.pyrosetta.org/'
+description = """
+PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling
+suite. It enables users to design their own custom molecular modeling algorithms using Rosetta
+sampling methods and energy functions.
+"""
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchainopts = {'usempi': True}
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('Python', '3.11.3'),
+]
+
+use_pip = True
+
+local_source_tmpl = '%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2'
+local_source_urls = 'https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python311.linux/'
+
+exts_list = [
+    (name, version, {
+        'source_tmpl': local_source_tmpl,
+        'source_urls': [local_source_urls],
+        'start_dir': 'setup',
+        'checksums': ['42a10efd16cba7739d87a5c4035a2cd8792bc193804963fc26bb2f82f7ac2a1a'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'