environment.yml

# Readme:
# Installation of this environment requires the typical correct paths to the databases
# we can create the environment with the following command:
# mamba env update -f environment.yml --prefix /raid/cache/biomols-public/environments/mlr_colabfold_202408
# mamba activate /raid/cache/biomols-public/environments/mlr_colabfold_202408
# pip install -e . --no-deps
# pip install --no-deps alphafold-colabfold
name: mlr_colabfold_202408
channels:
  - nodefaults
  - bioconda
  - conda-forge
dependencies:
  - python>=3.9,<3.12
  - pip
  # deep learning
  - cudatoolkit=11.8.0
  - nvidia::cuda-nvcc
  - jax=0.4.23
  - jaxlib=0.4.23=cuda*
  - tensorflow
  - dm-tree
  - dm-haiku
  # domain stuff
  - openmm==8.0
  - pdbfixer
  - kalign2
  - hhsuite
  - mmseqs2
  - biopython
  - pandas
  # misc
  - appdirs
  - tqdm
  - immutabledict
  - chex
  - absl-py
  - jupyter
  - pytest
  - pip:
    - ml-collections
    # - alphafold-colabfold
# we still need to install colabfold manually afterwards without dependencies!