helixfold3.def

Bootstrap: docker
From: nvidia/cuda:12.6.0-cudnn-devel-ubuntu24.04

%labels
    Author j.caley@unsw.edu.au
    Version 1.0.0

%post
    apt update && DEBIAN_FRONTEND=noninteractive apt install --no-install-recommends -y wget git

    wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"
    bash Miniforge3-Linux-x86_64.sh -b -p /opt/miniforge
    rm Miniforge3-Linux-x86_64.sh
    export PATH="/opt/miniforge/bin:$PATH"

    git clone --single-branch --branch dev --depth 1 --no-checkout https://github.com/PaddlePaddle/PaddleHelix.git app/helixfold3
    cd app/helixfold3
    git sparse-checkout init --cone
    git sparse-checkout set apps/protein_folding/helixfold3
    git checkout dev
    mv apps/protein_folding/helixfold3/* .
    rm -rf apps
    mamba env create -f environment.yaml

    apt autoremove -y && apt remove --purge -y wget git && apt clean -y
    rm -rf /var/lib/apt/lists/* /root/.cache *.tar.gz
    mamba clean --all --force-pkgs-dirs -y

%environment
    export PATH="/app/helixfold3:/opt/miniforge/bin:/opt/miniforge/envs/helixfold/bin:$PATH"
    export PYTHONPATH="/app/helixfold3:$PYTHONPATH"
    export PYTHON_BIN="/opt/miniforge/envs/helixfold/bin/python3.9"
    export ENV_BIN="/opt/miniforge/envs/helixfold/bin"
    export OBABEL_BIN="/opt/miniforge/envs/helixfold/bin"

%runscript
    mamba run --name helixfold "$@"