diff --git a/472_Geneformer/Geneformer-0.1.0-20241204-foss-2023a.eb b/472_Geneformer/Geneformer-0.1.0-20241204-foss-2023a.eb new file mode 100644 index 00000000..f74dc186 --- /dev/null +++ b/472_Geneformer/Geneformer-0.1.0-20241204-foss-2023a.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'Geneformer' +version = '0.1.0-20241204' +local_commit = '09de197' + +homepage = 'https://huggingface.co/ctheodoris/Geneformer' +description = """Geneformer is a foundational transformer model pretrained on a large-scale +corpus of single cell transcriptomes to enable context-aware predictions in settings +with limited data in network biology.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('HF-Datasets', '2.18.0'), + ('loompy', '3.0.7'), + ('matplotlib', '3.7.2'), + ('Optuna', '3.5.0'), + ('Arrow', '14.0.1'), + ('Ray-project', '2.9.1'), + ('scanpy', '1.9.8'), + ('scikit-learn', '1.3.1'), + ('Seaborn', '0.13.2'), + ('statsmodels', '0.14.1'), + ('tensorboard', '2.15.1'), + ('PyTorch', '2.1.2'), + ('tqdm', '4.66.1'), + ('Transformers', '4.39.3'), + ('accelerate', '0.33.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('optuna_integration', '4.1.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d6ce0ffb650f7783e6cc4a4fd2f684fb1252db441414669b14c01f65b1556a2c'], + }), + ('peft', '0.13.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d4e0951ec78eac11c45a051801c569913436888c578d48e5ce86996b715bc6ef'], + }), + ('accumulation_tree', '0.6.4', { + 'checksums': ['5f907667e4106b5ba140b6b871e1902eb2a93d429b92f8a9f7ddb2bee7704334'], + }), + ('pyudorandom', '1.0.0', { + 'checksums': ['f30a093a0170c15f9c7f87eb29f71f0f5fde995528b7c6dc4606d389e8c37755'], + }), + ('tdigest', '0.5.2.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['dd25f8d6e6be002192bba9e4b8c16491d36c10b389f50637818603d1f67c6fb2'], + }), + (name, version, { + 'sources': [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://huggingface.co/ctheodoris', + 'repo_name': name, + 'commit': local_commit, + }, + }], + 'checksums': [None], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + + +moduleclass = 'bio' diff --git a/472_Geneformer/accelerate-0.33.0-foss-2023a.eb b/472_Geneformer/accelerate-0.33.0-foss-2023a.eb new file mode 100644 index 00000000..65b13726 --- /dev/null +++ b/472_Geneformer/accelerate-0.33.0-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'accelerate' +version = '0.33.0' + +homepage = 'https://github.com/huggingface/accelerate' +description = """A simple way to launch, train, and use PyTorch models on almost any device and +distributed configuration, automatic mixed precision (including fp8), +and easy-to-configure FSDP and DeepSpeed support.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('PyTorch-bundle', '2.1.2'), + ('PyYAML', '6.0'), + ('Safetensors', '0.4.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('huggingface-hub', '0.24.5', { + 'sources': ['huggingface_hub-%(version)s.tar.gz'], + 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], + }), + (name, version, { + 'checksums': ['11ba481ed6ea09191775df55ce464aeeba67a024bd0261a44b77b30fb439e26a'], + }), +] + +sanity_check_commands = ['accelerate test'] + +moduleclass = 'ai'