install_dependencies.sh

#!/bin/bash
# 
# Copyright 2021 Beijing DP Technology Co., Ltd.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#      http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

# Shell script for installing the environment.
# Usage: bash install_dependencies.sh

#######################################
# dependencies of feature processing  #
#######################################

# install conda packages
conda install -y -c conda-forge openmm=7.5.1 pdbfixer cudatoolkit=11.1
conda install -y -c bioconda hmmer hhsuite==3.3.0 kalign2

# update openmm
work_path=$(pwd)
python_path=$(which python)
cd $(dirname $(dirname $python_path))/lib/python3.8/site-packages
patch -p0 < $work_path/openmm.patch
cd $work_path

#######################################
# dependencies of training Uni-Fold   #
#######################################

# install openmpi
wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.gz
gunzip -c openmpi-4.1.1.tar.gz | tar xf -
cd openmpi-4.1.1
./configure --prefix=/usr/local
make all install
cd ..

# install conda and pip packages
conda install -y -c nvidia cudnn==8.0.4
pip install --upgrade pip \
    && pip install -r ./requirements.txt \
    && pip install jaxlib==0.1.67+cuda111 -f \
    https://storage.googleapis.com/jax-releases/jax_releases.html