Dockerfile

FROM ubuntu:18.04

# ARGUMENTS
###########
ARG OPENSTRUCTURE_VERSION="python3_port"
ARG SRC_FOLDER="/usr/local/src"
ARG CPUS_FOR_MAKE=2
ARG OPENSTRUCTURE_SHARE="/usr/local/share/ost"
ARG MSMS_VERSION="2.6.1"
ARG OPENMM_VERSION="7.1.1"
ARG OPENMM_INCLUDE_PATH="/usr/local/openmm/include/"
ARG OPENMM_LIB_PATH="/usr/local/openmm/lib/"
ARG DEBIAN_FRONTEND=noninteractive

# INSTALL SYSTEM DEPS
#####################
RUN apt-get update -y && apt-get install -y cmake \
                                            g++ \
                                            gfortran \
                                            wget \
                                            tar \
                                            libsqlite3-dev \
                                            sip-dev \
                                            libtiff-dev \
                                            libfftw3-dev \
                                            libeigen3-dev \
                                            libboost-all-dev \
                                            libpng-dev \
                                            qt5-qmake \
                                            qtbase5-dev \
                                            python3-all \
                                            python3-pyqt5 \
                                            python3-numpy \
                                            python3-scipy \
                                            python3-pandas \
                                            doxygen \
                                            swig \
                                            clustalw \
                                            dssp \
                                            locales && \
                                            # CLEANUP
                                            rm -rf /var/lib/apt/lists/*

# INSTALL MSMS
##############
RUN cd ${SRC_FOLDER} && \
    mkdir -p msms && \
    cd ${SRC_FOLDER}/msms && \
    wget http://mgltools.scripps.edu/downloads/tars/releases/MSMSRELEASE/REL${MSMS_VERSION}/msms_i86_64Linux2_${MSMS_VERSION}.tar.gz && \
    tar -xvzf msms_i86_64Linux2_${MSMS_VERSION}.tar.gz && \
    cp -v ${SRC_FOLDER}/msms/msms.x86_64Linux2.${MSMS_VERSION} /usr/local/bin/msms && \
    cp -v ${SRC_FOLDER}/msms/pdb_to_xyzr /usr/local/bin/pdb_to_xyzr && \
    cp -v ${SRC_FOLDER}/msms/pdb_to_xyzrn /usr/local/bin/pdb_to_xyzrn && \
    rm -rf ${SRC_FOLDER}/msms

# INSTALL OPENMM
################
RUN cd ${SRC_FOLDER} && \
    wget -O openmm-${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 && \
    python3 setup.py build && python3 setup.py install && \
    rm ${SRC_FOLDER}/openmm-${OPENMM_VERSION}.tar.gz && \
    rm -rf ${SRC_FOLDER}/openmm-${OPENMM_VERSION}

# INSTALL OST
#############
RUN cd ${SRC_FOLDER} && \
    # copy ost release
    wget -O openstructure-${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 .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython3.6m.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 && \
    make -j ${CPUS_FOR_MAKE} && \
    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 && \
    mkdir -p $OPENSTRUCTURE_SHARE && chmod a+rw -R $OPENSTRUCTURE_SHARE && mv compounds.chemlib $OPENSTRUCTURE_SHARE && \
    cmake .. -DCOMPOUND_LIB=$OPENSTRUCTURE_SHARE/compounds.chemlib && \
             make -j ${CPUS_FOR_MAKE} && make check && make install && \
    rm ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}.tar.gz && \
    rm -rf ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}

# ENVIRONMENT
#############
WORKDIR /home
ENV OST_ROOT="/usr/local"
ENV PYTHONPATH="/usr/local/lib64/python3.6/site-packages"
ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64:/usr/local/openmm/lib/"
ENV QT_X11_NO_MITSHM=1
ENV OPENSTRUCTURE_VERSION=$OPENSTRUCTURE_VERSION

ENTRYPOINT ["ost"]
CMD ["-i"]