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Dockerfile
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# Build image:
# docker build --tag ghcr.io/biosimulators/biosimulators_tellurium/tellurium:2.1.6 --tag ghcr.io/biosimulators/biosimulators_tellurium/tellurium:latest .
#
# Run image:
# docker run \
# --tty \
# --rm \
# --mount type=bind,source="$(pwd)"/tests/fixtures,target=/root/in,readonly \
# --mount type=bind,source="$(pwd)"/tests/results,target=/root/out \
# biosimulators/tellurium:latest \
# -i /root/in/BIOMD0000000297.omex \
# -o /root/out
# Base OS
FROM python:3.9-slim-buster
ARG VERSION="0.1.25"
ARG SIMULATOR_VERSION="2.2.10"
# metadata
LABEL \
org.opencontainers.image.title="tellurium" \
org.opencontainers.image.version="${SIMULATOR_VERSION}" \
org.opencontainers.image.description="Python-based environment for model building, simulation, and analysis that facilitates reproducibility of models in systems and synthetic biology" \
org.opencontainers.image.url="http://tellurium.analogmachine.org/" \
org.opencontainers.image.documentation="https://tellurium.readthedocs.io/" \
org.opencontainers.image.source="https://github.com/biosimulators/Biosimulators_tellurium" \
org.opencontainers.image.authors="BioSimulators Team <info@biosimulators.org>" \
org.opencontainers.image.vendor="BioSimulators Team" \
org.opencontainers.image.licenses="Apache-2.0" \
\
base_image="python:3.9-slim-buster" \
version="${VERSION}" \
software="tellurium" \
software.version="${SIMULATOR_VERSION}" \
about.summary="Python-based environment for model building, simulation, and analysis that facilitates reproducibility of models in systems and synthetic biology" \
about.home="http://tellurium.analogmachine.org/" \
about.documentation="https://tellurium.readthedocs.io/" \
about.license_file="https://github.com/sys-bio/tellurium/blob/develop/LICENSE.txt" \
about.license="SPDX:Apache-2.0" \
about.tags="kinetic modeling,dynamical simulation,systems biology,biochemical networks,SBML,SED-ML,COMBINE,OMEX,BioSimulators" \
maintainer="BioSimulators Team <info@biosimulators.org>"
# Install requirements
RUN apt-get update -y \
&& apt-get install -y --no-install-recommends \
libxml2 \
libncurses5 \
&& apt-get autoremove -y \
&& rm -rf /var/lib/apt/lists/*
# fonts for matplotlib
RUN apt-get update -y \
&& apt-get install -y --no-install-recommends libfreetype6 \
&& rm -rf /var/lib/apt/lists/*
# Copy code for command-line interface into image and install it
COPY . /root/Biosimulators_tellurium
RUN pip install /root/Biosimulators_tellurium \
&& mkdir -p /.cache/matplotlib \
&& mkdir -p /.config/matplotlib \
&& chmod ugo+rw /.config/matplotlib \
&& chmod ugo+rw /.cache/matplotlib \
&& rm -rf /root/Biosimulators_tellurium
RUN pip install tellurium==${SIMULATOR_VERSION}
# Configure matplotlib backend
ENV PLOTTING_ENGINE=matplotlib \
MPLBACKEND=PDF \
PYTHONWARNINGS="ignore:The 'warn' parameter of use():UserWarning:tellurium.tellurium,ignore:Matplotlib is currently using agg:UserWarning:tellurium.plotting.engine_mpl" \
VERBOSE=0
# Entrypoint
ENTRYPOINT ["biosimulators-tellurium"]
CMD []