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| # Worker microservice ORIGINAL CONTENT | ||
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| FROM ghcr.io/biosimulators/bio-check-base:latest | ||
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| # os deps | ||
| RUN apt-get update && apt-get install -y libatlas-base-dev \ | ||
| libhdf5-serial-dev \ | ||
| swig \ | ||
| libboost-all-dev \ | ||
| git \ | ||
| meson \ | ||
| build-essential \ | ||
| g++ \ | ||
| gfortran \ | ||
| libblas-dev \ | ||
| liblapack-dev \ | ||
| gcc \ | ||
| gfortran \ | ||
| libgfortran5 | ||
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| # PySCeS | ||
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| # SUNDIALS --> installation path is default cmake (/usr/local) with LD_LIBRARY_PATH as runtime location | ||
| # ignore certificate checking because certificate was expired as of 2021-11-10 | ||
| ARG SUNDIALS_VERSION=2.6.2 | ||
| RUN apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| cmake \ | ||
| make \ | ||
| g++ \ | ||
| \ | ||
| && cd /tmp \ | ||
| && wget --no-check-certificate https://computing.llnl.gov/sites/default/files/inline-files/sundials-${SUNDIALS_VERSION}.tar.gz \ | ||
| && tar xvvf sundials-${SUNDIALS_VERSION}.tar.gz \ | ||
| && cd sundials-${SUNDIALS_VERSION} \ | ||
| && mkdir build \ | ||
| && cd build \ | ||
| && CFLAGS="-fPIC" cmake .. \ | ||
| && make \ | ||
| && make install \ | ||
| \ | ||
| && cd /tmp \ | ||
| && rm sundials-${SUNDIALS_VERSION}.tar.gz \ | ||
| && rm -r sundials-${SUNDIALS_VERSION} | ||
| ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH | ||
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| ############################################ | ||
| # App content | ||
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| COPY . /app/worker | ||
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| ENV PATH="/root/.local/bin:$PATH" | ||
| ENV TEST_SBML_FP="test_fixtures/Elowitz-Nature-2000-Repressilator/BIOMD0000000012_url.xml" | ||
| ENV TEST_OMEX_FP="test_fixtures/Elowitz-Nature-2000-Repressilator.omex" | ||
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| # copy pysces config | ||
| RUN mkdir -p /Pysces \ | ||
| && mkdir -p /Pysces/psc \ | ||
| && mkdir -p /root/Pysces \ | ||
| && mkdir -p /root/Pysces/psc \ | ||
| && chmod ugo+rw -R /Pysces | ||
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| COPY ./.pys_usercfg.ini /Pysces/.pys_usercfg.ini | ||
| COPY ./.pys_usercfg.ini /root/Pysces/.pys_usercfg.ini | ||
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| # Install only worker deps TODO: include toml in base deps | ||
| RUN poetry install --only=worker,pysces --no-cache | ||
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| # Install Assimulo from source for Pysces | ||
| # RUN apt-get update \ | ||
| # && apt-get install -y libblas-dev \ | ||
| # liblapack-dev \ | ||
| # libatlas-base-dev \ | ||
| # python3-distutils \ | ||
| # python3-dev \ | ||
| # && git clone https://github.com/modelon-community/Assimulo.git \ | ||
| # && cd Assimulo \ | ||
| # && poetry run pip install --upgrade setuptools pip wheel Cython numpy \ | ||
| # && poetry run python3 setup.py install --sundials-home=/usr/local --blas-home=/usr/lib/x86_64-linux-gnu | ||
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| # install masspy TODO: implement this | ||
| # RUN apt-get install -y --no-install-recommends \ | ||
| # git \ | ||
| # gcc \ | ||
| # build-essential \ | ||
| # libfreetype6-dev \ | ||
| # libfreetype6 \ | ||
| # pkg-config \ | ||
| # \ | ||
| # && mkdir -p /.cache/cobrapy | ||
| # RUN git clone https://github.com/biosimulators/Biosimulators_MASSpy.git \ | ||
| # && cd Biosimulators_MASSpy \ | ||
| # && rm pyproject.toml | ||
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| WORKDIR /app/worker | ||
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| RUN python3 -c "import os;files=os.listdir();import shutil;[shutil.rmtree(f) if '__pycache__' in f else None for f in files]" | ||
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| ENTRYPOINT ["poetry", "run", "python3", "main.py"] | ||
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| ############################# | ||
| # Fenics | ||
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| # TODO: start the fenics implementation | ||
| # RUN apt-get update && apt-get install -y petsc-dev \ | ||
| # libopenmpi-dev \ | ||
| # libspdlog-dev \ | ||
| # libpugixml-dev \ | ||
| # cmake \ | ||
| # gcc \ | ||
| # g++ \ | ||
| # gfortran \ | ||
| # && rm -rf /var/lib/apt/lists/* \ | ||
| # && add-apt-repository ppa:fenics-packages/fenics -y \ | ||
| # && apt update \ | ||
| # && apt install -y fenicsx \ | ||
| # && poetry run pip install meson-python meson ninja | ||
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| # RUN poetry run pip install \ | ||
| # biosimulators-utils[logging] \ | ||
| # biosimulators-amici \ | ||
| # biosimulators-copasi \ | ||
| # biosimulators-pysces \ | ||
| # biosimulators-tellurium | ||
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| # add deps with extras | ||
| # RUN yes | poetry cache clear PyPI --all \ | ||
| # && poetry add biosimulators-utils --extras=logging \ | ||
| # && poetry add pysces --extras=sbml \ | ||
| # && poetry add biosimulators-copasi --python="^3.10" | ||
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| # install requirements in poetry via pip prox | ||
| # RUN poetry run pip install -r /app/worker/requirements.worker.txt | ||
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| # install masspy TODO: do this | ||
| # RUN poetry run pip install biosimulators-masspy | ||
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| # install with poetry TODO: remove this eventually | ||
| # RUN /app/assets/install_deps.sh /app/worker/requirements.worker.txt |
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