alphafold.def

Bootstrap: localimage
From: base.sif

# Build instructions from
# https://github.com/kalininalab/alphafold_non_docker
# Note: Versions of Python packages removed in order to resolve outdated and missing for Python 3.8

%files
    run.sh /opt/run.sh

%post
    # miniconda setup
    cd /opt/
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
    source /opt/miniconda3/etc/profile.d/conda.sh
    conda create --name alphafold python=3.8
    conda update -n base conda
    conda activate alphafold

    conda install -y -c conda-forge openmm cudnn cudatoolkit pdbfixer
    conda install -y -c bioconda hmmer hhsuite kalign2

    # alphafold setup
    cd /opt/
    git clone https://github.com/deepmind/alphafold.git
    # alphafold_path="/opt/alphafold"

    wget -q -P alphafold/alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt

    pip install absl-py biopython chex dm-haiku dm-tree immutabledict jax ml-collections numpy pandas scipy tensorflow
    pip install --upgrade jax jaxlib -f https://storage.googleapis.com/jax-releases/jax_releases.html
    pip install -r alphafold/requirements.txt

    # Originally, AlphaFold pins OpenMM to 7.5.1, an old version that is no longer supported.
    # It also requires applying a patch (file docker/openmm.patch in the official AlphaFold git repository) related to disulfide bonds.
    # Newer versions of OpenMM include that fix and so the patch isn't needed anymore.
    # AlphaFold Issues - https://github.com/deepmind/alphafold/issues/404#issue-1172485609

    # cd /opt/miniconda3/envs/alphafold/lib/python3.8/site-packages/ && patch -p0 < $alphafold_path/docker/openmm.patch

    mv /opt/run.sh /opt/alphafold/run.sh