DiMA/environment.yaml at main · AIRI-Institute/DiMA · GitHub

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name: dima_env
channels:
  - pytorch
  - nvidia
  - bioconda
  - salilab
  - conda-forge
  - defaults
dependencies:
  - python=3.10
  - pip=23.0
  - gxx_linux-64>=9,<=12
  - ninja
  - cuda=12.1.0
  - cuda-nvcc=12.6.20
  - cuda-version=12.6
  - cuda-toolkit=12.1.0
  - cuda-compiler=12.6.2
  - pytorch=2.5.1
  - pytorch-cuda=12.1
  - torchvision=0.20.1
  - torchmetrics=1.6.0
  - libxcrypt
  - bioconda::tmalign
  - matplotlib=3.7.1
  - numpy=1.24.3
  - pandas=2.0.1
  - scipy
  - jupyter
  - ipython
  - ipykernel
  - pip:
    - accelerate==0.29.3
    - argparse==1.4.0
    - ml-collections==0.1.1
    - nltk==3.8.1
    - scikit-image==0.21.0
    - scikit-learn==1.3.2
    - seaborn==0.12.2
    - timm==0.9.16
    - tqdm==4.66.3
    - transformers==4.40.0
    - wandb==0.15.0
    - datasets==3.6.0
    - huggingface_hub==0.24.0
    - evaluate
    - biopython==1.81
    - biotite==0.37.0
    - sentencepiece==0.1.99
    - hydra-core>=1.3
    - lightning
    - einops
    - numba
    - dm-tree
    - modelcif
    - omegaconf
    - h5py
    - lmdb
    - safetensors
    - py3Dmol
    - pyarrow
    - plotly
    - ninja
    - git+https://github.com/facebookresearch/esm.git@d7b3331f41442ed4ffde70cb95bdd48cabcec2e9
    - git+https://github.com/amyxlu/evo.git
    - git+https://github.com/MeshchaninovViacheslav/cheap-proteins.git
    - git+https://github.com/amyxlu/openfold.git