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environment.yml
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environment.yml
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name: tdc-conda-env
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- anndata=0.6.22
- biopython=1.78
- dataclasses=0.8
- fuzzywuzzy=0.18.0
- huggingface_hub=0.20.3
- mygene=3.2.2
- numpy=1.26.4
- openpyxl=3.0.10
- python=3.10
- pip=23.3.1
- pandas=2.1.4
- requests=2.31.0
- scikit-learn=1.2.2
- seaborn=0.12.2
- tqdm=4.65.0
- pip:
- accelerate==0.33.0
- cellxgene-census==1.15.0
- datasets==2.20.0
- dgl==1.1.3
- evaluate==0.4.2
- gget==0.28.4
- moleculeace==3.0.0
- pydantic==2.6.3
- gget==0.28.4
- pydantic==2.6.3
- gget==0.28.4
- pydantic==2.6.3
- pytest==8.3.2
- rdkit==2023.9.5
- tiledbsoma==1.11.4
- torch==2.1.1
- torch_geometric==2.5.3
- torchvision==0.16.1
- transformers==4.43.4
- yapf==0.40.2
- git+https://github.com/amva13/geneformer.git@main#egg=geneformer
variables:
KMP_DUPLICATE_LIB_OK: "TRUE"