AlphaFold.def

Bootstrap: docker
From: nvidia/cuda:11.1.1-cudnn8-runtime-ubuntu18.04
# Edit CUDA version here and in %post

%environment
export PATH="/opt/conda/bin${PATH:+:${PATH}}"

%files
# Build on ../
alphafold /app/alphafold

%post -c /bin/bash

  # Setup CUDA version
  CUDA=11.1.1

  apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
    build-essential \
    cmake \
    cuda-command-line-tools-$(cut -f1,2 -d- <<< ${CUDA//./-}) \
    git \
    hmmer \
    kalign \
    locales \
    tzdata \
    wget
  
  rm -rf /var/lib/apt/lists/*

  locale-gen "en_US.UTF-8"

  git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /opt/hh-suite 
  mkdir -p /opt/hh-suite/build 
  cd /opt/hh-suite/build 
  cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. 
  make -j 4 && make install 
  ln -s /opt/hhsuite/bin/* /usr/bin 
  cd /
  rm -rf /opt/hh-suite

  #wget -q -P /opt https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 
  #bash /opt/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda 
  wget -q -P /opt https://repo.anaconda.com/miniconda/Miniconda3-py310_24.1.2-0-Linux-x86_64.sh
  bash /opt/Miniconda3-py310_24.1.2-0-Linux-x86_64.sh -b -p /opt/conda 
  rm -f /opt/Miniconda3-py310_24.1.2-0-Linux-x86_64.sh

  export PATH="/opt/conda/bin${PATH:+:${PATH}}"

  conda install -qy conda==24.1.2
  conda install -y -c conda-forge \
    openmm=7.7.0 \
	matplotlib=3.8.3 \
    cudatoolkit==${CUDA_VERSION} \
    pdbfixer \
    pip 
  conda clean --all --force-pkgs-dirs --yes

  ldconfig
  ldconfig -p

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

  pip3 install --upgrade pip --no-cache-dir 
  pip3 install -r /app/alphafold/requirements.txt --no-cache-dir 
  pip3 install --upgrade --no-cache-dir jax==0.3.25 jaxlib==0.3.25+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

  cd -

  cd /app/alphafold
  cat << 'EOF' > /app/run_alphafold.sh
#!/bin/bash

export LD_LIBRARY_PATH=/usr/local/cuda/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}
cd /app/alphafold
python /app/alphafold/run_alphafold.py "$@"
EOF

   chmod +xr /app/run_alphafold.sh

%runscript

  cd /app/alphafold
  exec  /app/run_alphafold.sh "$@"

%labels
AUTHOR esteva.m@wehi.edu.au