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Dockerfile
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# Base OS
FROM ghcr.io/biosimulators/biosimulators_pysces/pysces_base:latest
ARG VERSION=0.1.25
ARG SIMULATOR_VERSION="1.2.1"
# metadata
LABEL \
org.opencontainers.image.title="PySCeS" \
org.opencontainers.image.version="${SIMULATOR_VERSION}" \
org.opencontainers.image.description="Simulation and analysis tools for modelling biological systems" \
org.opencontainers.image.url="https://pysces.github.io/" \
org.opencontainers.image.documentation="https://pyscesdocs.readthedocs.io/" \
org.opencontainers.image.source="https://github.com/biosimulators/Biosimulators_PySCeS" \
org.opencontainers.image.authors="BioSimulators Team <info@biosimulators.org>" \
org.opencontainers.image.vendor="BioSimulators Team" \
org.opencontainers.image.licenses="BSD-3-Clause" \
\
base_image="python:3.10-slim-bookworm" \
version="${VERSION}" \
software="PySCeS" \
software.version="${SIMULATOR_VERSION}" \
about.summary="Simulation and analysis tools for modelling biological systems" \
about.home="https://pysces.github.io/" \
about.documentation="https://pyscesdocs.readthedocs.io/" \
about.license_file="https://github.com/PySCeS/pysces/blob/master/LICENSE" \
about.license="SPDX:BSD-3-Clause" \
about.tags="BioSimulators,mathematical model,kinetic model,simulation,systems biology,computational biology,SBML,SED-ML,COMBINE,OMEX" \
extra.identifiers.biotools="pysces" \
maintainer="BioSimulators Team <info@biosimulators.org>"
# install PySCeS
RUN apt-get update -y \
&& apt-get install -y --no-install-recommends \
libgfortran5 \
\
&& pip install "pysces[parscan,sbml]==${SIMULATOR_VERSION}" \
\
&& apt-get autoremove -y \
&& rm -rf /var/lib/apt/lists
# Copy code for command-line interface into image and install it
COPY . /root/Biosimulators_PySCeS
RUN pip install /root/Biosimulators_PySCeS \
&& mkdir -p /Pysces \
&& mkdir -p /Pysces/psc \
&& mkdir -p /root/Pysces \
&& mkdir -p /root/Pysces/psc \
&& chmod ugo+rw -R /Pysces \
&& cp /root/Biosimulators_PySCeS/.pys_usercfg.Dockerfile.ini /Pysces/.pys_usercfg.ini \
&& cp /root/Biosimulators_PySCeS/.pys_usercfg.Dockerfile.ini /root/Pysces/.pys_usercfg.ini \
&& rm -rf /root/Biosimulators_PySCeS
# supported environment variables
ENV ALGORITHM_SUBSTITUTION_POLICY=SIMILAR_VARIABLES \
VERBOSE=0 \
MPLBACKEND=PDF
# Entrypoint
ENTRYPOINT ["biosimulators-pysces"]
CMD []