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Dockerfile
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# Base OS
FROM python:3.9-slim-buster
ARG VERSION="0.0.9"
ARG SIMULATOR_VERSION=3.0.0b
# metadata
LABEL \
org.opencontainers.image.title="GINsim" \
org.opencontainers.image.version="${SIMULATOR_VERSION}" \
org.opencontainers.image.description="Tool for modeling and simulating genetic regulatory networks." \
org.opencontainers.image.url="http://ginsim.org/" \
org.opencontainers.image.documentation="http://doc.ginsim.org/" \
org.opencontainers.image.authors="BioSimulators Team <info@biosimulators.org>" \
org.opencontainers.image.vendor="BioSimulators Team" \
org.opencontainers.image.licenses="SPDX:GPL-3.0-only" \
\
base_image="python:3.9-slim-buster" \
version="${VERSION}" \
software="GINsim" \
software.version="${SIMULATOR_VERSION}" \
about.summary="Tool for modeling and simulating genetic regulatory networks." \
about.home="http://ginsim.org/" \
about.documentation="http://doc.ginsim.org/" \
about.license_file="http://choosealicense.com/licenses/gpl-3.0/" \
about.license="SPDX:GPL-3.0-only" \
about.tags="BioSimulators,mathematical model,logical model,simulation,systems biology,computational biology,SBML,SED-ML,COMBINE,OMEX" \
maintainer="BioSimulators Team <info@biosimulators.org>"
# fonts for matplotlib
RUN apt-get update -y \
&& apt-get install -y --no-install-recommends libfreetype6 \
&& rm -rf /var/lib/apt/lists/*
# Install GINsim
RUN apt-get update -y \
&& apt-get install -y --no-install-recommends \
default-jre \
wget \
\
&& cd /tmp \
&& pip install ginsim \
&& wget https://raw.githubusercontent.com/GINsim/GINsim-python/master/ginsim_setup.py \
&& python ginsim_setup.py \
\
&& rm ginsim_setup.py \
&& apt-get remove -y \
wget \
&& apt-get autoremove -y \
&& rm -rf /var/lib/apt/lists/*
# Copy code for command-line interface into image and install it
COPY . /root/Biosimulators_GINsim
RUN pip install /root/Biosimulators_GINsim \
&& rm -rf /root/Biosimulators_GINsim
RUN mkdir -p /.config/matplotlib \
&& mkdir -p /.cache/matplotlib \
&& chmod ugo+rw /.config/matplotlib \
&& chmod ugo+rw /.cache/matplotlib \
&& python -c "import matplotlib.font_manager"
ENV VERBOSE=0 \
MPLBACKEND=PDF
# Entrypoint
ENTRYPOINT ["biosimulators-ginsim"]
CMD []