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Dockerfile
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#FROM maven:3.5-jdk-8-alpine as build
#COPY . /app/
#WORKDIR /app
#RUN mvn clean install -DskipTests -Dmaven.test.skip=true --quiet dependency:copy-dependencies
#
#
## Base OS
#FROM ubuntu:latest
#
#ARG SIMULATOR_VERSION="7.4.0.23"
#
## metadata
#LABEL \
# org.opencontainers.image.title="VCell" \
# org.opencontainers.image.version="${SIMULATOR_VERSION}" \
# org.opencontainers.image.description="Open-source software package for modeling cell biological systems that is built on a central database and disseminated as a standalone application." \
# org.opencontainers.image.url="http://vcell.org/" \
# org.opencontainers.image.documentation="https://vcell.org/support" \
# org.opencontainers.image.source="https://github.com/virtualcell/vcell" \
# org.opencontainers.image.authors="BioSimulators Team <[email protected]>" \
# org.opencontainers.image.vendor="BioSimulators Team" \
# org.opencontainers.image.licenses="MIT" \
# base_image="ubuntu:latest" \
# version="${SIMULATOR_VERSION}" \
# software="Virtual Cell" \
# software.version="${SIMULATOR_VERSION}" \
# about.summary="Open-source software package for modeling cell biological systems that is built on a central database and disseminated as a standalone application." \
# about.home="http://vcell.org/" \
# about.documentation="https://vcell.org/support" \
# about.license_file="https://github.com/virtualcell/vcell/blob/master/license.txt" \
# about.license="SPDX:MIT" \
# about.tags="rule-based modeling,kinetic modeling,dynamical simulation,systems biology,BNGL,SED-ML,COMBINE,OMEX" \
# maintainer="BioSimulators Team <[email protected]>"
#
#RUN apt-get -y update && \
# apt-get install -y --no-install-recommends curl openjdk-8-jre dnsutils && \
# apt-get install -y python3 && \
# apt install -y python3-pip && \
# mkdir -p /usr/local/app/vcell/lib && \
# mkdir -p /usr/local/app/vcell/simulation && \
# mkdir -p /usr/local/app/vcell/installDir && \
# mkdir -p /usr/local/app/vcell/installDir/python/vcell_cli_utils
#
## Add linux local solvers only
#
#ADD ./nativelibs /usr/local/app/vcell/installDir/nativelibs
#COPY ./docker_run.sh /usr/local/app/vcell/installDir/
#
#
## Declare supported environment variables
#ENV ALGORITHM_SUBSTITUTION_POLICY=SIMILAR_VARIABLES
#
## Install required python-packages
#COPY ./vcell-cli-utils/ /usr/local/app/vcell/installDir/python/vcell_cli_utils/
#RUN pip3 install -r /usr/local/app/vcell/installDir/python/vcell_cli_utils/requirements.txt
#RUN pip3 install /usr/local/app/vcell/installDir/python/vcell_cli_utils/
#
#COPY --from=build /app/localsolvers /usr/local/app/vcell/installDir/localsolvers
## Copy JAR files
#COPY --from=build /app/vcell-client/target/vcell-client-0.0.1-SNAPSHOT.jar \
# /app/vcell-client/target/maven-jars/*.jar \
# /app/vcell-core/target/vcell-core-0.0.1-SNAPSHOT.jar \
# /app/vcell-core/target/maven-jars/*.jar \
# /app/vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \
# /app/vcell-server/target/maven-jars/*.jar \
# /app/vcell-vmicro/target/vcell-vmicro-0.0.1-SNAPSHOT.jar \
# /app/vcell-vmicro/target/maven-jars/*.jar \
# /app/vcell-oracle/target/vcell-oracle-0.0.1-SNAPSHOT.jar \
# /app/vcell-oracle/target/maven-jars/*.jar \
# /app/vcell-admin/target/vcell-admin-0.0.1-SNAPSHOT.jar \
# /app/vcell-admin/target/maven-jars/*.jar \
# /app/vcell-cli/target/vcell-cli-0.0.1-SNAPSHOT.jar \
# /app/vcell-cli/target/maven-jars/*.jar \
# /app/non-maven-java-libs/com/oracle/ojdbc6/11.2.0.4/ojdbc6-11.2.0.4.jar \
# /app/non-maven-java-libs/com/oracle/ucp/11.2.0.4/ucp-11.2.0.4.jar \
# /app/non-maven-java-libs/org/sbml/libcombine/libCombineLinux64/0.2.7/libCombineLinux64-0.2.7.jar \
# /usr/local/app/vcell/lib/
#RUN chmod -R 755 /usr/local/app/vcell && chmod +x /usr/local/app/vcell/installDir/docker_run.sh
#
## Entrypoint
#ENTRYPOINT ["/usr/local/app/vcell/installDir/docker_run.sh"]
#CMD []
FROM ubuntu
ARG SIMULATOR_VERSION="7.4.0.23"
# metadata
LABEL \
org.opencontainers.image.title="VCell" \
org.opencontainers.image.version="${SIMULATOR_VERSION}" \
org.opencontainers.image.description="Open-source software package for modeling cell biological systems that is built on a central database and disseminated as a standalone application." \
org.opencontainers.image.url="http://vcell.org/" \
org.opencontainers.image.documentation="https://vcell.org/support" \
org.opencontainers.image.source="https://github.com/biosimulators/Biosimulators_VCell" \
org.opencontainers.image.authors="BioSimulators Team <[email protected]>" \
org.opencontainers.image.vendor="BioSimulators Team" \
org.opencontainers.image.licenses="MIT" \
\
base_image="ubuntu:18.04" \
version="${SIMULATOR_VERSION}" \
software="Virtual Cell" \
software.version="${SIMULATOR_VERSION}" \
about.summary="Open-source software package for modeling cell biological systems that is built on a central database and disseminated as a standalone application." \
about.home="http://vcell.org/" \
about.documentation="https://vcell.org/support" \
about.license_file="https://github.com/virtualcell/vcell/blob/master/license.txt" \
about.license="SPDX:MIT" \
about.tags="rule-based modeling,kinetic modeling,dynamical simulation,systems biology,BNGL,SED-ML,COMBINE,OMEX" \
maintainer="BioSimulators Team <[email protected]>"
RUN apt-get -y update && \
apt-get install -y --no-install-recommends curl openjdk-8-jre dnsutils && \
apt-get install -y python3 && \
apt install -y python3-pip && \
mkdir -p /usr/local/app/vcell/lib && \
mkdir -p /usr/local/app/vcell/simulation && \
mkdir -p /usr/local/app/vcell/installDir && \
mkdir -p /usr/local/app/vcell/installDir/python/vcell_cli_utils
# Copy JAR files
COPY ./vcell-client/target/vcell-client-0.0.1-SNAPSHOT.jar \
./vcell-client/target/maven-jars/*.jar \
./vcell-core/target/vcell-core-0.0.1-SNAPSHOT.jar \
./vcell-core/target/maven-jars/*.jar \
./vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \
./vcell-server/target/maven-jars/*.jar \
./vcell-vmicro/target/vcell-vmicro-0.0.1-SNAPSHOT.jar \
./vcell-vmicro/target/maven-jars/*.jar \
./vcell-oracle/target/vcell-oracle-0.0.1-SNAPSHOT.jar \
./vcell-oracle/target/maven-jars/*.jar \
./vcell-admin/target/vcell-admin-0.0.1-SNAPSHOT.jar \
./vcell-admin/target/vcell-admin-0.0.1-SNAPSHOT-tests.jar \
./vcell-admin/target/maven-jars/*.jar \
./vcell-cli/target/vcell-cli-0.0.1-SNAPSHOT.jar \
./vcell-cli/target/maven-jars/*.jar \
./non-maven-java-libs/com/oracle/ojdbc6/11.2.0.4/ojdbc6-11.2.0.4.jar \
./non-maven-java-libs/com/oracle/ucp/11.2.0.4/ucp-11.2.0.4.jar \
./non-maven-java-libs/org/sbml/libcombine/libCombineLinux64/0.2.7/libCombineLinux64-0.2.7.jar \
/usr/local/app/vcell/lib/
COPY ./vcell-cli-utils/ /usr/local/app/vcell/installDir/python/vcell_cli_utils/
# Install required python-packages
RUN which pip3
RUN pip3 install -r /usr/local/app/vcell/installDir/python/vcell_cli_utils/requirements.txt
#RUN pip3 install vcell_cli_utils
# Add linux local solvers only
ADD ./localsolvers /usr/local/app/vcell/installDir/localsolvers
ADD ./nativelibs /usr/local/app/vcell/installDir/nativelibs
COPY ./docker_run.sh /usr/local/app/vcell/installDir/
# Declare supported environment variables
ENV ALGORITHM_SUBSTITUTION_POLICY=SIMILAR_VARIABLES
# Entrypoint
ENTRYPOINT ["/usr/local/app/vcell/installDir/docker_run.sh"]
CMD []