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Dockerfile-base
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Dockerfile-base
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# FROM ghcr.io/biosimulators/biosimulators:latest
FROM ghcr.io/vivarium-collective/biosimulator-processes:0.0.4
LABEL authors="alexanderpatrie"
ENV DEBIAN_FRONTEND=noninteractive
ENV MONGO_URI="mongodb://mongodb/?retryWrites=true&w=majority&appName=bio-check"
# handle app creds from google
RUN mkdir /.google
COPY ./assets/.biosimulations.json /.google/.bio-check.json
# COPY ./.bio-check.json /.google/.bio-check.json
# hdf5/amici deps
RUN apt-get update \
&& apt-get install -y libatlas-base-dev libhdf5-serial-dev swig libboost-all-dev \
&& rm -rf /var/lib/apt/lists/*
# handle main content
WORKDIR /app
RUN mkdir /app/data
# copy deps
COPY ./assets/requirements.base.txt ./assets/scripts/remove_deps.sh ./assets/scripts/update_deps.sh ./assets/dropped.txt ./assets/scripts/install_deps.sh /app/assets/
# copy example files TODO: optimize this.
COPY ./model-examples/sbml-core/Elowitz-Nature-2000-Repressilator.omex /app/data/Elowitz-Nature-2000-Repressilator.omex
COPY ./model-examples/sbml-core/Elowitz-Nature-2000-Repressilator /app/data/Elowitz-Nature-2000-Repressilator
RUN chmod +x /app/assets/install_deps.sh \
&& /app/assets/install_deps.sh /app/assets/requirements.base.txt
# RUN poetry add $(cat /app/assets/requirements.base.txt)
# RUN chmod +x /app/assets/remove_deps.sh \
# && chmod +x /app/assets/update_deps.sh \
# && pip install --upgrade pip \
# && /app/assets/remove_deps.sh \
# && pip install --no-cache-dir -r /app/assets/requirements.base.txt \
# && pip install --upgrade google-cloud-storage
# shared tooling module
# COPY ./assets/shared.py /app/shared.py