Dockerfile

# HiCBrowser

FROM nginx

MAINTAINER Björn A. Grüning, bjoern.gruening@gmail.com

ARG HICBROWSER_RELEASE
ARG HICBROWSER_REPO

ENV HICBROWSER_RELEASE=${HICBROWSER_RELEASE:-uwsgi} \
    HICBROWSER_REPO=${HICBROWSER_REPO:-https://github.com/maxplanck-ie/HiCBrowser} \
    HICBROWSER_ROOT=/home/hicbrowser \
    HICBROWSER_CONDA_PREFIX=/home/hicbrowser/conda \
    HICBROWSER_USER=hicbrowser \
    HICBROWSER_UID=1450 \
    HICBROWSER_GID=1450 \
    HICBROWSER_HOME=/home/hicbrowser

RUN apt-get update && apt-get install -y \
  wget \
  supervisor \
  bzip2 \
  unzip \
  nano \
  net-tools && \
  apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Make NGINX run on the foreground
#RUN echo "daemon off;" >> /etc/nginx/nginx.conf

#RUN locale-gen en_US.UTF-8 && dpkg-reconfigure locales
ENV PATH=$HICBROWSER_CONDA_PREFIX/bin:$PATH

# Install Miniconda
RUN echo 'export PATH=$HICBROWSER_CONDA_PREFIX/bin:$PATH' > /etc/profile.d/conda.sh && \
    wget --quiet https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
    /bin/bash ~/miniconda.sh -b -p $HICBROWSER_CONDA_PREFIX && \
    rm ~/miniconda.sh

RUN conda install hicexplorer=1.8.1 uwsgi bx-python python-lzo pysam flask==0.10.1 python=2.7 -c conda-forge -c bioconda -c anaconda
RUN pip install pip==8.1.2 && pip install $HICBROWSER_REPO/archive/$HICBROWSER_RELEASE.tar.gz && \
    mkdir master && wget https://github.com/maxplanck-ie/HiCBrowser/archive/master.tar.gz && \
    tar zxvf master.tar.gz HiCBrowser-master/example_browser && \
    mv HiCBrowser-master/example_browser /data/ && \
    rm master.tar.gz HiCBrowser-master -rf

# Custom Supervisord config
COPY supervisord.conf /etc/supervisor/conf.d/supervisord.conf
COPY monitor_traffic.sh /monitor_traffic.sh

# Copy the modified Nginx conf
COPY nginx.conf /etc/nginx/conf.d/

# Copy the base uWSGI ini file to enable default dynamic uwsgi process number
COPY uwsgi.ini /etc/uwsgi/
COPY startup.sh /usr/bin/startup

# Remove default configuration from Nginx
RUN rm /etc/nginx/conf.d/default.conf && \
    chmod +x /monitor_traffic.sh /usr/bin/startup

EXPOSE 80

# Mark folders as imported from the host.
VOLUME ["/data/"]

# Autostart script that is invoked during container start
CMD ["/usr/bin/startup"]