data/Dockerfile

FROM eclipse-temurin:17-jammy as jre-build

# Create a custom Java runtime
RUN $JAVA_HOME/bin/jlink \
         --add-modules ALL-MODULE-PATH \
         --strip-debug \
         --no-man-pages \
         --no-header-files \
         --compress=2 \
         --output /javaruntime

# Define base image and copy in jlink created minimal Java 17 environment
FROM ubuntu:jammy
ENV JAVA_HOME=/opt/java/openjdk
ENV PATH "${JAVA_HOME}/bin:${PATH}"
COPY --from=jre-build /javaruntime $JAVA_HOME

# now we have Java 17 and Python 3.9
ARG SIMULATOR_VERSION="7.5.0.11"
ARG MAX_JAVA_MEM=0
# Make sure you don't sap all of docker's memory when you set this.
ENV ENV_SIMULATOR_VERSION=$SIMULATOR_VERSION
ENV MAX_JAVA_MEM_MB=$MAX_JAVA_MEM

# metadata
LABEL \
    org.opencontainers.image.title="VCell" \
    org.opencontainers.image.version="${SIMULATOR_VERSION}" \
    org.opencontainers.image.description="Open-source software package for modeling cell biological systems that is built on a central database and disseminated as a standalone application." \
    org.opencontainers.image.url="http://vcell.org/" \
    org.opencontainers.image.documentation="https://vcell.org/support" \
    org.opencontainers.image.source="https://github.com/biosimulators/Biosimulators_VCell" \
    org.opencontainers.image.authors="BioSimulators Team <info@biosimulators.org>" \
    org.opencontainers.image.vendor="BioSimulators Team" \
    org.opencontainers.image.licenses="MIT" \
    \
    base_image="ubuntu:22.04" \
    version="${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 <info@biosimulators.org>"

ENV DEBIAN_FRONTEND noninteractive
RUN apt -y update && apt install -y software-properties-common
RUN apt install -y --no-install-recommends curl python3.10 python3-pip build-essential dnsutils \
    apt-utils libfreetype6 fontconfig fonts-dejavu

RUN 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 && \
    mkdir -p /usr/local/app/vcell/installDir/bionetgen

RUN python3 -m pip install poetry &&  poetry config cache-dir "/poetry/.cache"
ENV PATH="/root/.poetry/bin:/root/.local/bin:$PATH"

# Copy JAR files
COPY ./vcell-cli/target/vcell-cli-0.0.1-SNAPSHOT.jar \
     ./vcell-cli/target/maven-jars/*.jar \
     /usr/local/app/vcell/lib/

# Install required python-packages
COPY ./vcell-cli-utils/ /usr/local/app/vcell/installDir/python/vcell_cli_utils/
RUN cd /usr/local/app/vcell/installDir/python/vcell_cli_utils/ && \
    poetry config cache-dir "/poetry/.cache" --local && \
    chmod 755 poetry.toml && \
    poetry install

# 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/
COPY ./bionetgen/BNG2.pl ./bionetgen/*.txt ./bionetgen/VERSION /usr/local/app/vcell/installDir/bionetgen/
COPY ./bionetgen/Perl2 /usr/local/app/vcell/installDir/bionetgen/Perl2
COPY ./biosimulations_log4j2.xml /usr/local/app/vcell/installDir/

# Declare supported environment variables
ENV ALGORITHM_SUBSTITUTION_POLICY=SIMILAR_VARIABLES
EXPOSE 1433


# Entrypoint
ENTRYPOINT ["/usr/local/app/vcell/installDir/docker_run.sh"]
CMD []