environment.yml

name: tdc-conda-env 
channels:
  - bioconda
  - conda-forge
  - defaults
  - dglteam
  - pyg
  - pytorch
dependencies:
  - anndata=0.6.22
  - biopython=1.78
  - dataclasses=0.8
  - dgl=2.1.0
  - fuzzywuzzy=0.18.0
  - huggingface_hub=0.20.3
  - mygene=3.2.2
  - numpy=1.26.4
  - openpyxl=3.0.10
  - python=3.9.13
  - pip=23.3.1
  - pandas=2.1.4
  - pyg=2.5.0
  - pytorch=2.2.1
  - pyg=2.5.0
  - pytorch=2.2.1
  - requests=2.31.0
  - scikit-learn=1.2.2
  - seaborn=0.12.2
  - tqdm=4.65.0
  - torchaudio=2.2.1
  - torchvision=0.17.1
  - torchaudio=2.2.1
  - torchvision=0.17.1
  - pip:
    - cellxgene-census==1.10.2 
    - gget==0.28.4
    - pydantic==2.6.3
    - gget==0.28.4
    - pydantic==2.6.3
    - gget==0.28.4
    - pydantic==2.6.3
    - rdkit==2023.9.5
    - tiledbsoma==1.7.2
    - yapf==0.40.2
variables:
  KMP_DUPLICATE_LIB_OK: "TRUE"