Biosimulators_VCell/docker/build/Dockerfile-data-dev at dev · shoops/Biosimulators_VCell · GitHub

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# VTK and OpenJDK n Alpine Linux
#FROM alpine:3.7
# Install some Alpine packages
#RUN apk add --no-cache \
#    bash \
#    build-base \
#    cmake \
#    wget \
#    mesa-dev \
#    mesa-osmesa \
#    python2-dev
# Download and extract VTK source, then configure and build VTK
#RUN wget -nv -O- http://www.vtk.org/files/release/7.1/VTK-7.1.0.tar.gz | \
#    tar xz && \
#    cd VTK-7.1.0 && \
#    cmake \
#    -D CMAKE_BUILD_TYPE:STRING=Release \
#    -D CMAKE_INSTALL_PREFIX:STRING=/usr \
#    -D BUILD_DOCUMENTATION:BOOL=OFF \
#    -D BUILD_EXAMPLES:BOOL=OFF \
#    -D BUILD_TESTING:BOOL=OFF \
#    -D BUILD_SHARED_LIBS:BOOL=ON \
#    -D VTK_USE_X:BOOL=OFF \
#    -D VTK_OPENGL_HAS_OSMESA:BOOL=ON \
#    -D OSMESA_LIBRARY=/usr/lib/libOSMesa.so.8 \
#    -D OSMESA_INCLUDE_DIR=/usr/include/GL/ \
#    -D VTK_RENDERING_BACKEND:STRING=OpenGL \
#    -D VTK_Group_MPI:BOOL=OFF \
#    -D VTK_Group_StandAlone:BOOL=OFF \
#    -D VTK_Group_Rendering:BOOL=ON \
#    -D VTK_WRAP_PYTHON=ON \
#    -D VTK_PYTHON_VERSION:STRING=2 \
#    . && \
#    make -j 2 && \
#    make install && \
#    cd .. && rm -rf VTK-7.1.0
# install thrift python package
#RUN wget https://bootstrap.pypa.io/get-pip.py \
#    && python get-pip.py \
#    && pip install thrift
#RUN apk update && apk upgrade && \
#    apk add openjdk8 && \
#    mkdir /tmp/tmprt && \
#    cd /tmp/tmprt && \
#    apk add zip && \
#    unzip -q /usr/lib/jvm/default-jvm/jre/lib/rt.jar && \
#    apk add zip && \
#    zip -q -r /tmp/rt.zip . && \
#    apk del zip && \
#    cd /tmp && \
#    mv rt.zip /usr/lib/jvm/default-jvm/jre/lib/rt.jar && \
#    rm -rf /tmp/tmprt /var/cache/apk/* bin/jjs bin/keytool bin/orbd bin/pack200 bin/policytool \
#    bin/rmid bin/rmiregistry bin/servertool bin/tnameserv bin/unpack200

FROM schaff/vtk-openjdk-alpine:latest

RUN mkdir -p /usr/local/app && \
	apk update && \
	apk add --no-cache ttf-dejavu && \
    apk add openssh-client && \
    apk add screen

WORKDIR /usr/local/app

COPY ./vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \
     ./vcell-server/target/maven-jars/*.jar \
     ./lib/


COPY ./pythonScripts ./pythonScripts
COPY ./nativelibs/linux64 ./nativelibs/linux64
COPY ./docker/build/vcell-data.log4j.xml .

ENV softwareVersion=SOFTWARE-VERSION-NOT-SET \
	serverid=SITE \
    jmshost_int_internal=activemqint \
    jmsport_int_internal=61616 \
    jmsuser=clientUser \
	mongodb_host_internal=mongodb \
	mongodb_port_internal=27017 \
    mongodb_database=test \
    export_baseurl="export-baseurl-not-set" \
    simdatadir_external=/path/to/external/simdata/ \
    jmsblob_minsize=100000 \
    simdataCacheSize="simdataCacheSize-not-set" \
    servertype="servertype-not-set"

ENV jmspswdfile=/run/secrets/jmspswd

VOLUME /simdata
VOLUME /share/apps/vcell10/users
VOLUME /exportdir

EXPOSE 8000

ENTRYPOINT java \
	-Xdebug -Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=n \
	-XX:+UnlockExperimentalVMOptions -XX:+UseCGroupMemoryLimitForHeap -XX:MaxRAMFraction=1 -Xms64M \
    -Djava.awt.headless=true \
	-Dvcell.softwareVersion="${softwareVersion}" \
	-Djava.util.logging.manager=org.apache.logging.log4j.jul.LogManager \
	-Dlog4j.configurationFile=/usr/local/app/vcell-data.log4j.xml \
	-Dvcell.server.id="${serverid}" \
	-Dvcell.python.executable=/usr/bin/python \
	-Dvcell.primarySimdatadir.internal=/simdata \
	-Dvcell.primarySimdatadir.external="${simdatadir_external}" \
	-Dvcell.simdataCacheSize="${simdataCacheSize}" \
	-Dvcell.export.baseDir.internal=/exportdir/ \
	-Dvcell.export.baseURL="${export_baseurl}" \
	-Dvcell.installDir=/usr/local/app \
	-Dvcell.jms.int.host.internal="${jmshost_int_internal}" \
	-Dvcell.jms.int.port.internal="${jmsport_int_internal}" \
	-Dvcell.jms.blobMessageUseMongo=true \
	-Dvcell.jms.blobMessageMinSize="${jmsblob_minsize}" \
	-Dvcell.jms.user="${jmsuser}" \
	-Dvcell.jms.pswdfile="${jmspswdfile}" \
	-Dvcell.mongodb.host.internal=${mongodb_host_internal} \
	-Dvcell.mongodb.port.internal=${mongodb_port_internal} \
	-Dvcell.mongodb.database=${mongodb_database} \
	-cp "./lib/*" cbit.vcell.message.server.data.SimDataServer \
	"${servertype}"