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FROM condaforge/miniforge3:24.9.2-0
LABEL org.opencontainers.image.title="bio-compose-server-base" \
org.opencontainers.image.description="Base Docker image for BioCompose REST API management, job processing, and datastorage with MongoDB, ensuring scalable and robust performance." \
org.opencontainers.image.url="https://compose.biosimulators.org/" \
org.opencontainers.image.source="https://github.com/biosimulators/bio-compose-server" \
org.opencontainers.image.authors="Alexander Patrie <[email protected]>, BioSimulators Team <[email protected]>" \
org.opencontainers.image.vendor="BioSimulators Team"
# SHELL ["/usr/bin/env", "bash", "-c"]
ENV DEBIAN_FRONTEND=noninteractive
# copy assets
COPY assets/docker/config/.biosimulations.json /.google/.bio-compose.json
COPY assets/docker/config/.pys_usercfg.ini /Pysces/.pys_usercfg.ini
COPY assets/docker/config/.pys_usercfg.ini /root/Pysces/.pys_usercfg.ini
COPY tests/test_fixtures /test_fixtures
WORKDIR /app
# copy container libs
# COPY ./gateway /bio-compose-server/gateway
# COPY ./shared /bio-compose-server/shared
# COPY ./worker /bio-compose-server/worker
# copy env configs
COPY ./environment.yml /app/environment.yml
COPY ./pyproject.toml /app/pyproject.toml
COPY ./shared/scripts/entrypoint.sh /app/entrypoint.sh
# COPY . /app
RUN echo "Server" > /app/README.md \
&& mkdir /app/config \
&& chmod +x /app/entrypoint.sh
#
RUN conda update -n base -c conda-forge conda \
&& conda env create -f /app/environment.yml -y \
&& conda run -n server poetry self update \
&& echo "conda activate server" >> /.bashrc \
&& conda run -n server pip install --upgrade pip
# && conda run -n server pip install --no-cache-dir git+https://github.com/vivarium-collective/process-bigraph.git@main
ENTRYPOINT ["/bin/bash"]
# ENTRYPOINT ["/app/entrypoint.sh"]
# RUN apt-get update \
# && apt-get install -y \
# meson \
# g++ \
# gfortran \
# libblas-dev \
# liblapack-dev \
# libgfortran5 \
# libhdf5-dev \
# libhdf5-serial-dev \
# libatlas-base-dev \
# cmake \
# make \
# git \
# build-essential \
# python3-dev \
# swig \
# libc6-dev \
# libx11-dev \
# libc6 \
# libgl1-mesa-dev \
# pkg-config \
# curl \
# tar \
# libgl1-mesa-glx \
# libice6 \
# libsm6 \
# gnupg \
# libstdc++6
# RUN conda update -n base -c conda-forge conda \
# && conda env create -f /bio-compose-server/environment.yml -y \
# && conda run -n server pip install --upgrade pip \
# && echo "conda activate server" >> /.bashrc \
# && conda run -n server poetry config virtualenvs.create false \
# && conda run -n server poetry lock \
# && conda run -n server poetry install
# && conda config --env --add channels conda-forge \
# && conda config --set channel_priority strict \
# && conda install readdy \
# && conda env create -f environment.yml -y
# && conda install -c conda-forge pymem3dg -y \
# && echo 'export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:\$LD_LIBRARY_PATH' >> ~/.bashrc