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2.1.1
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Bootstrap: docker
From: containers.las.iastate.edu/centos8-cuda11.0-cudnn8-tensorrt7-python38-tensorflow
%environment
export PATH=$PATH:/opt/hhsuite/bin:/opt/hmmer/bin:/opt/kalign/bin:/opt/openmm/bin:/usr/local/cuda/bin
export LD_LIBRARY_PATH=/usr/local/cuda/lib64
%post -c /bin/bash
set -e
dnf install -y git cmake patch automake autoconf opencl-headers gcc-gfortran fftw-devel swig doxygen
mkdir /build
# build hmmer
cd /build
curl -LO http://eddylab.org/software/hmmer/hmmer-3.3.2.tar.gz
tar -xzf hmmer-3.3.2.tar.gz
cd hmmer-3.3.2
./configure --prefix=/opt/hmmer
make -j16
make install
for i in $(ls /opt/hmmer/bin); do ln -s /opt/hmmer/bin/$i /usr/bin/$i; done;
# build kalign
cd /build
curl -LO https://github.com/TimoLassmann/kalign/archive/refs/tags/v3.3.1.tar.gz
tar -xzf v3.3.1.tar.gz
cd kalign-3.3.1
./autogen.sh
./configure --prefix=/opt/kalign
make -j16
make install
for i in $(ls /opt/kalign/bin); do ln -s /opt/kalign/bin/$i /usr/bin/$i; done;
#build hhsuite
cd /build
git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git
mkdir hh-suite/build
cd hh-suite/build
cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite ..
make -j16
make install
for i in $(ls /opt/hhsuite/bin); do ln -s /opt/hhsuite/bin/$i /usr/bin/$i; done;
cd /build
# build openmm
python3 -m pip install --upgrade cython
curl -LO https://github.com/openmm/openmm/archive/refs/tags/7.5.1.tar.gz
tar -xzf 7.5.1.tar.gz
cd openmm-7.5.1
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=/opt/openmm -DCMAKE_LIBRARY_PATH=/usr/local/cuda/lib64/stubs
make -j16
make install
make PythonInstall
for i in $(ls /opt/openmm/bin); do ln -s /opt/openmm/bin/$i /usr/bin/$i; done;
# pdbfixer
curl -LO https://github.com/openmm/pdbfixer/archive/refs/tags/v1.7.tar.gz
tar -xzf v1.7.tar.gz
cd pdbfixer-1.7
python3 -m pip install .
#alphafold proper
git clone -b v2.1.1 https://github.com/deepmind/alphafold.git /opt/alphafold
cd /opt/alphafold
curl -vL https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt -o alphafold/common/stereo_chemical_props.txt
python3 -m pip install --upgrade pip
python3 -m pip install -r requirements.txt
python3 -m pip install --upgrade jax jaxlib==0.1.69+cuda110 -f https://storage.googleapis.com/jax-releases/jax_releases.html
#patch openMM
cd /opt/python38/lib/python3.8/site-packages/
patch -p0 < /opt/alphafold/docker/openmm.patch
chmod -R o+rX /opt
rm -rf /build
dnf remove -y git cmake automake autoconfig autotools
dnf clean all
rm -rf /var/cache/dnf/*
set +e