Compilation and Installation

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Go to the source package directory.

   cd /path/to/AlphaFold

3. Decompress the installation package.

   tar -xvf alphaFold-xxx.tar.gz

   

   xxx indicates the software version.

4. Go to the directory generated after the decompression.

   cd alphafold

5. Perform the installation.

   pip3 install --upgrade pip
   && pip3 install -r ./requirements.txt
   && pip3 install --upgrade "jax[cuda111]" -f
   https://storage.googleapis.com/jax-releases/jax_releases.html
   && pip3 install jaxlib==0.1.70+cuda111 -f
   https://storage.googleapis.com/jax-releases/jax_releases.html
   # work_path=/path/to/alphafold-code
   work_path=$(PWD)
   # update openmm
   a=$(which python)
   cd $(dirname $(dirname $a))/lib/python3.8/site-packages
   patch -p0 < $work_path/docker/openmm.patch

6. Download the database script.

   wget https://github.com/kalininalab/alphafold_non_docker/blob/main/download_db.sh

7. Download the alphafold_data file.

   bash download_db.sh -d </home/johndoe/alphafold_data>