pescobar/OpenStructure-Singularity:latest
$ singularity pull shub://pescobar/OpenStructure-Singularity:latest
Singularity Recipe
BootStrap: docker
From: centos:7.4.1708
%post
# DEFINE SOME ENV VARS USED DURING THE IMAGE BUILD
##########################
export OPENSTRUCTURE_VERSION="1.7.1"
export OST_ROOT=/usr/local
export PYTHONPATH=/usr/local/lib64/python2.7/site-packages
export EIGEN_VERSION="3.3.4"
export OPENMM_VERSION="6.1"
export OPENMM_INCLUDE_PATH=/usr/local/openmm/include/
export OPENMM_LIB_PATH=/usr/local/openmm/lib/
export SRC_FOLDER="/usr/local/src"
export CPUS_FOR_MAKE=1
# INSTALL SYSTEM DEPS
##########################
yum makecache fast
yum -y install epel-release
yum -y install \
boost-devel \
bzip2 \
cmake \
doxygen \
fftw-devel \
fftw-static \
file \
freetype-devel \
gcc \
gcc-c++ \
gcc-gfortran \
glibc-common \
glibc-devel \
libjpeg-turbo-devel \
libpng-devel \
libtiff-devel \
make \
mesa-libGL-devel \
mesa-libGLU-devel \
numpy \
PyQt4 \
python-devel \
qt-devel \
strace \
swig \
wget
# COPY EIGEN HEADER FILES TO /usr/local/include/Eigen
#########################
cd ${SRC_FOLDER}
if [ ! -f eigen-${EIGEN_VERSION}.tar.bz2 ]; then
wget -O eigen-${EIGEN_VERSION}.tar.bz2 -nc http://bitbucket.org/eigen/eigen/get/${EIGEN_VERSION}.tar.bz2
mkdir -p ${SRC_FOLDER}/eigen-${EIGEN_VERSION}
tar xf eigen-${EIGEN_VERSION}.tar.bz2 -C ${SRC_FOLDER}/eigen-${EIGEN_VERSION} --strip-components=1
cp -r ${SRC_FOLDER}/eigen-${EIGEN_VERSION}/Eigen/ /usr/local/include/
fi
# COMPILE OPENMM FROM SOURCES. INSTALL TO /usr/local
############################
cd ${SRC_FOLDER}
if [ ! -f openmm-${OPENMM_VERSION}.tar.gz ]; then
wget -O openmm-${OPENMM_VERSION}.tar.gz -nc https://github.com/pandegroup/openmm/archive/${OPENMM_VERSION}.tar.gz
mkdir ${SRC_FOLDER}/openmm-${OPENMM_VERSION}
tar xf openmm-${OPENMM_VERSION}.tar.gz -C ${SRC_FOLDER}/openmm-${OPENMM_VERSION} --strip-components=1
mkdir -p ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build && cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build
cmake .. && make -j $CPUS_FOR_MAKE && make install
cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build/python && python setup.py build && python setup.py install
fi
# COMPILE OST FROM SOURCES. INSTALL TO /usr/local
###########################
cd ${SRC_FOLDER}
if [ ! -f openstructure-${OPENSTRUCTURE_VERSION}.tar.gz ]; then
wget -O openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -nc https://git.scicore.unibas.ch/schwede/openstructure/repository/${OPENSTRUCTURE_VERSION}/archive.tar.gz
mkdir openstructure-${OPENSTRUCTURE_VERSION}
tar xf openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -C ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION} --strip-components=1
mkdir -p ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build && cd ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build
cmake .. \
-DENABLE_MM=1 \
-DOPEN_MM_LIBRARY=/usr/local/openmm/lib/libOpenMM.so \
-DOPEN_MM_PLUGIN_DIR=/usr/local/openmm/lib/plugins/ \
-DOPEN_MM_INCLUDE_DIR=/usr/local/openmm/include/ \
-DCOMPILE_TMTOOLS=1 \
-DENABLE_GFX=ON \
-DENABLE_GUI=OFF \
-DUSE_NUMPY=1 \
-DUSE_RPATH=1 \
-DEIGEN3_INCLUDE_DIR=/usr/local/include/Eigen/ \
-DFFTW_LIBRARY=/usr/lib64/libfftw3f.a \
-DQT_QMAKE_EXECUTABLE=/usr/lib64/qt4/bin/qmake \
-DOPTIMIZE=1
make -j ${CPUS_FOR_MAKE}
make check
make install
fi
yum clean all
rm -rf /var/cache/yum
%environment
export OST_ROOT=/usr/local
export PYTHONPATH=/usr/local/lib64/python2.7/site-packages
export LC_ALL="en_US.UTF-8"
%apprun chemdict_tool
/usr/local/bin/chemdict_tool
%apprun lddt
/usr/local/bin/lddt
%apprun molck
/usr/local/bin/molck
%apprun ost
/usr/local/bin/ost
%apprun tmalign
/usr/local/bin/tmalign
%apprun tmscore
/usr/local/bin/tmscore
%runscript
/usr/local/bin/ost
Collection
- Name: pescobar/OpenStructure-Singularity
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/pescobar-OpenStructure-Singularity-latest |
collection name | pescobar/OpenStructure-Singularity |
branch | master |
tag | latest |
commit | a9e58280820058e06195506b7d7e72aceedcfb1e |
version (container hash) | 3f2a8823b2f83e70be05dce0c4cdb970 |
build date | 2018-03-01T23:01:16.601Z |
size (MB) | 1391 |
size (bytes) | 421580831 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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