Dockerfile.jobs

FROM python:2.7

# Install package dependencies for jobs
RUN apt-get -qq update && \
    apt-get -qq install --no-install-recommends \
      pkg-config \
      libpng-dev \
      libfreetype6-dev \
      libblas-dev \
      liblapack-dev \
      gfortran \
      netcat \
      libatlas-base-dev \
      libhdf5-dev \
      python-tk \
      r-base \
      r-base-dev \
      libffi-dev \
      libssl-dev && \
    apt-get -qq clean all && \
    apt-get -qq autoclean && \
    apt-get -qq autoremove && \
    rm -rf /var/lib/apt/lists/*

# Configure our app's expected working directory
ENV BASEDIR="/app" \
    PYTHONPATH="$BASEDIR"
WORKDIR $BASEDIR/

# Install Python dependencies for jobs (1/2)
# force setuptools v33; newer versions will fail https://github.com/pypa/setuptools/issues/937
# alternative is to update pip, but that requires updating python (otherwise we
# hit security errors), and that's complicated, because ubuntu 14.04 locks in
# 2.7.6
COPY requirements $BASEDIR/requirements/
RUN pip --no-cache-dir install -q setuptools==33.1.1
RUN pip --no-cache-dir install -q numpy==1.11.3
RUN pip --no-cache-dir install -q -r requirements/nest_jobs.txt

# Install Python dependencies for jobs (2/2)
# The following pip packages do not declare their dependencies properly, and
# therefore cannot reliably be installed from the requirements txt files.
# (pip does not install in the order declared in the file, but rather
# an ordering based on installing the order to resolve dependencies)
RUN pip --no-cache-dir install -q biom-format==2.1.5
RUN pip --no-cache-dir install -q h5py==2.5.0 && \
    python -c "import skbio"   #this prevents a "caching fonts" message on every command

# Copy in demo files, publication data, and pipeline readmes
WORKDIR /
RUN git clone https://github.com/KnowEnG/quickstart-demos && \
    cp -r quickstart-demos/demo_files / && \
    cp -r quickstart-demos/publication_data /demo_files/ && \
    find /demo_files -type f -name \*.bz2 | xargs bzip2 -d && \
    cp -r quickstart-demos/pipeline_readmes / && \
    rm -rf /quickstart-demos
WORKDIR $BASEDIR/

COPY . .

# Define our jobs worker entrypoint
ENTRYPOINT ["python","-m","nest_py.knoweng.jobs.worker_app"]