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