environment.yml

name: fastfold
channels:
  - conda-forge
  - bioconda
  - pytorch
dependencies:
  - pip:
      - biopython==1.79
      - dm-tree==0.1.6
      - ml-collections==0.1.0
      - numpy==1.21.2
      - PyYAML==5.4.1
      - requests==2.26.0
      - scipy==1.7.1
      - tqdm==4.62.2
      - typing-extensions==3.10.0.2
      - einops
      - colossalai
      - --find-links https://download.pytorch.org/whl/cu113/torch_stable.html torch==1.11.1+cu113
      - --find-links https://download.pytorch.org/whl/cu113/torch_stable.html torchaudio==0.11.1+cu113
      - --find-links https://download.pytorch.org/whl/cu113/torch_stable.html torchvision==0.13.1
  - conda-forge::python=3.8
  - conda-forge::setuptools=59.5.0
  - conda-forge::pip
  - conda-forge::openmm=7.5.1
  - conda-forge::pdbfixer
  - bioconda::hmmer==3.3.2
  - bioconda::hhsuite==3.3.0
  - bioconda::kalign2==2.04