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Commit 6a3ee355 authored by Studer Gabriel's avatar Studer Gabriel
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updated Dockerfile

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...@@ -2,67 +2,47 @@ FROM ubuntu:18.04 ...@@ -2,67 +2,47 @@ FROM ubuntu:18.04
# ARGUMENTS # ARGUMENTS
########### ###########
ARG OPENSTRUCTURE_VERSION="python3_port"
ARG OPENSTRUCTURE_VERSION="1.10.0"
ARG SRC_FOLDER="/usr/local/src" ARG SRC_FOLDER="/usr/local/src"
ARG CPUS_FOR_MAKE=8 ARG CPUS_FOR_MAKE=2
ARG PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
ARG OPENSTRUCTURE_SHARE="/usr/local/share/ost" ARG OPENSTRUCTURE_SHARE="/usr/local/share/ost"
ARG MSMS_VERSION="2.6.1" ARG MSMS_VERSION="2.6.1"
ARG OPENMM_VERSION="7.1.1" ARG OPENMM_VERSION="7.1.1"
ARG DSSP_VERSION="2.2.1"
ARG OPENMM_INCLUDE_PATH="/usr/local/openmm/include/" ARG OPENMM_INCLUDE_PATH="/usr/local/openmm/include/"
ARG OPENMM_LIB_PATH="/usr/local/openmm/lib/" ARG OPENMM_LIB_PATH="/usr/local/openmm/lib/"
ARG DEBIAN_FRONTEND=noninteractive
# INSTALL SYSTEM DEPS # INSTALL SYSTEM DEPS
##################### #####################
RUN apt-get update -y && apt-get install -y cmake \ RUN apt-get update -y && apt-get install -y cmake \
g++ \ g++ \
gfortran \
wget \
tar \
libsqlite3-dev \
sip-dev \ sip-dev \
libtiff-dev \ libtiff-dev \
libfftw3-dev \ libfftw3-dev \
libeigen3-dev \ libeigen3-dev \
libboost-all-dev \ libboost-all-dev \
libpng-dev \ libpng-dev \
python-all \
python2.7 \
python-pyqt5 \
qt5-qmake \ qt5-qmake \
qtbase5-dev \ qtbase5-dev \
wget \ python3-all \
git \ python3-pyqt5 \
gfortran \ python3-numpy \
python-pip \ python3-scipy \
tar \ python3-pandas \
libbz2-dev \
doxygen \ doxygen \
swig \ swig \
clustalw \ clustalw \
python-virtualenv \
libsqlite3-dev \
dssp \ dssp \
python-enum34 \
locales && \ locales && \
# CLEANUP # CLEANUP
rm -rf /var/lib/apt/lists/* rm -rf /var/lib/apt/lists/*
# INSTALL SOME PYTHON PACKAGES GLOBALY # INSTALL MSMS
###################################### ##############
RUN pip install -U pip==9.0.3 && \
pip install -U setuptools==39.0.1 && \
pip install --no-cache-dir numpy==1.10.4 \
scipy==1.0.0 \
pandas==0.22.0
# SET LOCALE
############
# RUN echo "LC_ALL=en_US.UTF-8" >> /etc/environment
# RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
# RUN echo "LANG=en_US.UTF-8" > /etc/locale.conf
# RUN locale-gen en_US.UTF-8
# DOWNLOAD AND INSTALL MSMS
###########################
RUN cd ${SRC_FOLDER} && \ RUN cd ${SRC_FOLDER} && \
mkdir -p msms && \ mkdir -p msms && \
cd ${SRC_FOLDER}/msms && \ cd ${SRC_FOLDER}/msms && \
...@@ -73,8 +53,8 @@ RUN cd ${SRC_FOLDER} && \ ...@@ -73,8 +53,8 @@ RUN cd ${SRC_FOLDER} && \
cp -v ${SRC_FOLDER}/msms/pdb_to_xyzrn /usr/local/bin/pdb_to_xyzrn && \ cp -v ${SRC_FOLDER}/msms/pdb_to_xyzrn /usr/local/bin/pdb_to_xyzrn && \
rm -rf ${SRC_FOLDER}/msms rm -rf ${SRC_FOLDER}/msms
# COMPILE OPENMM FROM SOURCES. INSTALL TO /usr/local # INSTALL OPENMM
#################################################### ################
RUN cd ${SRC_FOLDER} && \ RUN cd ${SRC_FOLDER} && \
wget -O openmm-${OPENMM_VERSION}.tar.gz -nc https://github.com/pandegroup/openmm/archive/${OPENMM_VERSION}.tar.gz && \ wget -O openmm-${OPENMM_VERSION}.tar.gz -nc https://github.com/pandegroup/openmm/archive/${OPENMM_VERSION}.tar.gz && \
mkdir ${SRC_FOLDER}/openmm-${OPENMM_VERSION} && \ mkdir ${SRC_FOLDER}/openmm-${OPENMM_VERSION} && \
...@@ -83,23 +63,20 @@ RUN cd ${SRC_FOLDER} && \ ...@@ -83,23 +63,20 @@ RUN cd ${SRC_FOLDER} && \
cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build && \ cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build && \
cmake .. && make -j $CPUS_FOR_MAKE && make install && \ cmake .. && make -j $CPUS_FOR_MAKE && make install && \
cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build/python && \ cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build/python && \
python setup.py build && python setup.py install && \ python3 setup.py build && python3 setup.py install && \
rm -rf ${SRC_FOLDER}/openmm-${OPENMM_VERSION}.tar.gz && \ rm ${SRC_FOLDER}/openmm-${OPENMM_VERSION}.tar.gz && \
rm -rf ${SRC_FOLDER}/openmm-${OPENMM_VERSION} rm -rf ${SRC_FOLDER}/openmm-${OPENMM_VERSION}
# INSTALL OST # INSTALL OST
############# #############
RUN cd ${SRC_FOLDER} && \ RUN cd ${SRC_FOLDER} && \
# copy ost release # copy ost release
wget -O openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -nc https://git.scicore.unibas.ch/schwede/openstructure/repository/${OPENSTRUCTURE_VERSION}/archive.tar.gz && \ wget -O openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -nc https://git.scicore.unibas.ch/schwede/openstructure/repository/${OPENSTRUCTURE_VERSION}/archive.tar.gz && \
mkdir openstructure-${OPENSTRUCTURE_VERSION} && \ mkdir openstructure-${OPENSTRUCTURE_VERSION} && \
tar xf openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -C ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION} --strip-components=1 && \ tar xf openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -C ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION} --strip-components=1 && \
mkdir -p ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build mkdir -p ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build && \
cd ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build && \
WORKDIR ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython3.6m.so \
# cmake ost
RUN cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
-DOPTIMIZE=ON \ -DOPTIMIZE=ON \
-DENABLE_MM=ON \ -DENABLE_MM=ON \
-DCOMPILE_TMTOOLS=1 \ -DCOMPILE_TMTOOLS=1 \
...@@ -109,52 +86,21 @@ RUN cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \ ...@@ -109,52 +86,21 @@ RUN cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
-DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \ -DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \
-DENABLE_GFX=ON \ -DENABLE_GFX=ON \
-DENABLE_GUI=ON && \ -DENABLE_GUI=ON && \
# Build chemdict_tool make -j ${CPUS_FOR_MAKE} && \
make -j ${CPUS_FOR_MAKE} chemdict_tool wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz && \
stage/bin/chemdict_tool create components.cif.gz compounds.chemlib pdb && stage/bin/chemdict_tool update ../modules/conop/data/charmm.cif compounds.chemlib charmm && \
# get the compound library mkdir -p $OPENSTRUCTURE_SHARE && chmod a+rw -R $OPENSTRUCTURE_SHARE && mv compounds.chemlib $OPENSTRUCTURE_SHARE && \
RUN wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz cmake .. -DCOMPOUND_LIB=$OPENSTRUCTURE_SHARE/compounds.chemlib && \
RUN stage/bin/chemdict_tool create components.cif.gz compounds.chemlib pdb && stage/bin/chemdict_tool update ../modules/conop/data/charmm.cif compounds.chemlib charmm make -j ${CPUS_FOR_MAKE} && make check && make install && \
RUN mkdir -p $OPENSTRUCTURE_SHARE && chmod a+rw -R $OPENSTRUCTURE_SHARE && mv compounds.chemlib $OPENSTRUCTURE_SHARE rm ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}.tar.gz && \
rm -rf ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}
# Build and install OST
RUN cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
-DOPTIMIZE=ON \
-DENABLE_MM=ON \
-DCOMPILE_TMTOOLS=1 \
-DUSE_NUMPY=1 \
-DOPEN_MM_LIBRARY=$OPENMM_LIB_PATH/libOpenMM.so \
-DOPEN_MM_INCLUDE_DIR=$OPENMM_INCLUDE_PATH \
-DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \
-DENABLE_GFX=ON \
-DENABLE_GUI=ON \
-DCOMPOUND_LIB=$OPENSTRUCTURE_SHARE/compounds.chemlib && \
# Build OST with compound library
make -j ${CPUS_FOR_MAKE} && make check && make install
# GO HOME AND CLEANUP
#####################
# RUN apt-get purge -y cmake \
# wget \
# git \
# gfortran \
# python-pip \
# libbz2-dev \
# doxygen \
# swig
# RUN apt-get clean
# RUN apt-get autoremove -y
#
# WORKDIR $SRC_FOLDER
# RUN rm -rf $SRC_FOLDER/*
WORKDIR /home
# ENVIRONMENT # ENVIRONMENT
############################################################################## #############
WORKDIR /home
ENV OST_ROOT="/usr/local" ENV OST_ROOT="/usr/local"
ENV PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}" ENV PYTHONPATH="/usr/local/lib64/python3.6/site-packages"
ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64" ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64:/usr/local/openmm/lib/"
ENV QT_X11_NO_MITSHM=1 ENV QT_X11_NO_MITSHM=1
ENTRYPOINT ["ost"] ENTRYPOINT ["ost"]
......
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