adding easyconfigs: ESM-2-2.0.0-foss-2023a-CUDA-12.1.1.eb, topaz-0.2.…

…5.20231120-foss-2023a-CUDA-12.1.1.eb, torchvision-0.16.2-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a-CUDA-12.1.1.eb

@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'ESM-2'
+version = '2.0.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/facebookresearch/esm'
+description = """ESM-2 outperforms all tested single-sequence protein language models
+ across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate
+ accurate structure predictions end to end directly from the sequence of a protein."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('Java', '11', '', SYSTEM),  # needed by ANTLR4 runtime
+]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('PyTorch', '2.1.2', versionsuffix),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+# omegaconf is required for esmfold (in addition to OpenFold-1.0.1)
+exts_list = [
+    ('antlr4-python3-runtime', '4.9.3', {
+        'modulename': 'antlr4',
+        'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'],
+    }),
+    ('omegaconf', '2.3.0', {
+        'checksums': ['d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7'],
+    }),
+    ('fair-esm', version, {
+        'modulename': "esm, esm.pretrained",
+        'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'],
+    }),
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/t/topaz/topaz-0.2.5.20231120-foss-2023a-CUDA-12.1.1.eb

@@ -0,0 +1,55 @@
+# Thomas Hoffman, EMBL Heidelberg, [email protected], 2023/11 
+easyblock = 'PythonPackage'
+
+name = 'topaz'
+_mainversion = '0.2.5'
+_commitdate = '20231120'
+_commit = '25cb2cb'
+version = '%s.%s' % (_mainversion, _commitdate)
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'http://cb.csail.mit.edu/cb/topaz/'
+
+description = """Particle picking software for single particle cryo-electron microscopy using    
+convolutional neural networks and positive-unlabeled learning. Includes methods
+for micrograph denoising."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('scikit-learn', '1.3.1'),
+    ('torchvision', '0.16.2', versionsuffix),
+]
+
+source_urls = ['https://github.com/tbepler/topaz/archive']
+sources = [{
+    'download_filename': '%s.tar.gz' % _commit,
+    'filename': '%(name)s-%(version)s.tar.gz'
+}]
+patches = [
+    'topaz-0.2.5_install_relion3_wrappers.patch',
+]
+checksums = [
+    {'topaz-0.2.5.20231120.tar.gz': 'ca0630f9a69622eb3e10c9de310f58ac846e60a5504c4533398a9a75b3091df9'},
+    {'topaz-0.2.5_install_relion3_wrappers.patch': '0fe23a0ecaf887aaa89641a7e7cf37fafd3134384b0a8f46acb4e17537d1a151'},
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+options = {'modulename': 'topaz'}
+
+_relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise']
+
+sanity_check_paths = {
+    'files': ["bin/run_topaz_%s.py" % x for x in _relion3_wrappers],
+    'dirs': [],
+}
+sanity_check_commands = ['run_topaz_%s.py --help' % x for x in _relion3_wrappers] + ['topaz --help']
+
+moduleclass = 'chem'

easybuild/easyconfigs/t/torchvision/torchvision-0.16.2-foss-2023a-CUDA-12.1.1.eb

@@ -0,0 +1,27 @@
+name = 'torchvision'
+version = '0.16.2'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/pytorch/vision'
+description = " Datasets, Transforms and Models specific to Computer Vision"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/pytorch/vision/archive']
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-0.16.2_ffmpeg-6.0-fix.patch']
+checksums = [
+    {'v0.16.2.tar.gz': '8c1f2951e98d8ada6e5a468f179af4be9f56d2ebc3ab057af873da61669806d7'},
+    {'torchvision-0.16.2_ffmpeg-6.0-fix.patch': 'a49336e7bfa1c950e886852bff37a3ea2146ac7bda87241e3ffb31c5cb869cce'},
+]
+
+builddependencies = [('CMake', '3.26.3')]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('Pillow-SIMD', '9.5.0'),
+    ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'),
+]
+
+moduleclass = 'vis'