Dockerfile

FROM jupyter/minimal-notebook
MAINTAINER "Christian Diener <mail [at] cdiener.com>"

USER root
RUN apt-get update -y && apt-get install -y wget libgmp-dev unzip && \
    apt-get clean && rm -rf /var/lib/apt/lists/*
USER jovyan

RUN conda update -yq --all && conda install -yq \
    Cython ipython biopython sympy numpy scipy nomkl pandas pytz && \
    pip install python-libsbml "cobra<=0.5.11" escher

# Build solplex extension
ENV SOPLEX_VERSION="3.0.0"
COPY soplex-$SOPLEX_VERSION.tgz /tmp
# Get soplex python extension
RUN cd /tmp && \
    wget https://github.com/SBRG/soplex_cython/archive/master.zip && \
    unzip master.zip && mv soplex_cython-master soplex_cython
# Compile patched soplex
RUN cd /tmp && \
    tar xvzf soplex-$SOPLEX_VERSION.tgz && mv soplex-$SOPLEX_VERSION soplex && \
    cd soplex/src && patch -b < /tmp/soplex_cython/long-double.patch && cd .. && \
    USRCPPFLAGS=" -DWITH_LONG_DOUBLE " make SHARED=true GMP=true ZLIB=false VERBOSE=true
# Build soplex python extension
RUN cd /tmp/soplex && ar crs libsoplex.a obj/*/lib/* && \
    mv libsoplex.a /tmp/soplex_cython && cd /tmp/soplex_cython && pip install .

# Install cobrame and ECOLIme
RUN pip install https://github.com/SBRG/cobrame/archive/master.zip \
                https://github.com/SBRG/ecolime/archive/master.zip
# Add example notebooks
RUN cd /home/jovyan/work && wget \
    https://github.com/SBRG/ecolime/raw/master/ecolime/build_ME_model.ipynb && \
    ln -s /opt/conda/lib/python3.5/site-packages/ecolime/build_ME_model.py

# Copy examples and clean up
RUN conda clean -tipsy
USER root
COPY getting_started.ipynb /home/jovyan/work
RUN mkdir /home/jovyan/work/me_models
COPY iLE1678.pickle /home/jovyan/work/me_models
RUN chown -R jovyan:users /home/jovyan/work/*
RUN rm -rf /tmp/*
USER jovyan