矩池云上安装AlphaFold教程

AlphaFold官方只提供了docker镜像，但是因为矩池云本身就是docker所以比较不方便。

项目官方地址：https://github.com/deepmind/alphafold

这里我是参考官方的Dockerfile来进行安装的：https://github.com/deepmind/alphafold/blob/main/docker/Dockerfile

apt安装依赖

apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
      build-essential \
      cmake \
      git \
      hmmer \
      kalign \
      tzdata \
      wget \
    && rm -rf /var/lib/apt/lists/*

创建虚拟环境

conda create -n alphafold python==3.8
conda update -n base conda
conda deactivate
conda activate alphafold

conda安装依赖

conda install -y -c conda-forge openmm==7.5.1 cudatoolkit=11.1 pdbfixer==1.7 pip
conda install -y -c bioconda hmmer==3.3.2 hhsuite==3.3.0 kalign2==2.04

git clone 仓库

git clone https://github.com/deepmind/alphafold.git
alphafold_path="/path/to/alphafold/git/repo"
wget -q -P alphafold/alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt

pip安装jax

pip install --upgrade pip \
    && pip install -r /alphafold/requirements.txt \
    && pip install --upgrade "jax[cuda111]" -f \
    https://storage.googleapis.com/jax-releases/jax_releases.html

添加OpenMM patch

cd ~/miniconda3/envs/alphafold/lib/python3.8/site-packages/ && patch -p0 < /alphafold/docker/openmm.patch

参考文章

https://github.com/deepmind/alphafold/blob/main/docker/Dockerfile

https://novopro.cn/articles/202107291210.html

https://github.com/kalininalab/alphafold_non_docker

https://github.com/deepmind/alphafold/issues/24

https://github.com/kuixu/alphafold