wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/app/ezhpc/conda
source /opt/app/ezhpc/conda/bin/activate
conda create --name alphafold python==3.8
conda activate alphafold
conda install -y -c conda-forge openmm==7.5.1 cudatoolkit-dev==11.2.2 cudatoolkit==11.2.2 pdbfixer
conda install -y -c bioconda hmmer hhsuite==3.3.0 kalign2
pip install absl-py==1.0.0 biopython==1.79 chex==0.0.7 dm-haiku==0.0.9 dm-tree==0.1.6 immutabledict==2.0.0 jax==0.3.25 ml-collections==0.1.0 numpy==1.21.6 pandas==1.3.4 protobuf==3.20.1 scipy==1.7.3 tensorflow-cpu==2.9.0
pip 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
mkdir -p /opt/app/ezhpc/alphafold/
curl https://codeload.github.com/deepmind/alphafold/tar.gz/refs/tags/v2.3.2 | tar zxvf -
mv alphafold-2.3.2 /opt/app/ezhpc/alphafold/2.3.2
wget --no-check-certificate -P /opt/app/ezhpc/alphafold/2.3.2/alphafold/common/ \
https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
cd /opt/app/ezhpc/conda/envs/alphafold/lib/python3.8/site-packages/
patch -p0 < /opt/app/ezhpc/alphafold/2.3.2/docker/openmm.patch
