Dockerfile

FROM r-base:3.5.1

ENV BRANCH 2.0.8

# Install.
RUN \
  apt-get update && \
  apt-get -y dist-upgrade && \
  apt-get install -y wget make devscripts apache2-dev apache2 libapreq2-dev r-base r-base-dev libapparmor-dev libcurl4-openssl-dev libprotobuf-dev protobuf-compiler xvfb xauth xfonts-base curl libssl-dev libxml2-dev libicu-dev pkg-config libssh2-1-dev locales apt-utils && \
  useradd -ms /bin/bash builder

# Note: this is different from Ubuntu (c.f. 'language-pack-en-base')
RUN localedef -i en_US -f UTF-8 en_US.UTF-8

USER builder

RUN \
  cd ~ && \
  wget https://github.com/opencpu/opencpu-server/archive/v${BRANCH}.tar.gz && \
  tar xzf v${BRANCH}.tar.gz && \
  cd opencpu-server-${BRANCH} && \
  dpkg-buildpackage -us -uc

USER root

RUN \
  apt-get install -y libapache2-mod-r-base && \
  dpkg -i /home/builder/opencpu-lib_*.deb && \
  dpkg -i /home/builder/opencpu-server_*.deb

RUN \
  apt-get install -y gdebi-core git sudo && \
  wget --quiet https://download2.rstudio.org/rstudio-server-stretch-1.1.456-amd64.deb && \
  gdebi --non-interactive rstudio-server-stretch-1.1.456-amd64.deb && \
  rm -f rstudio-server-stretch-1.1.456-amd64.deb && \
  echo "server-app-armor-enabled=0" >> /etc/rstudio/rserver.conf

# Prints apache logs to stdout
RUN \
  ln -sf /proc/self/fd/1 /var/log/apache2/access.log && \
  ln -sf /proc/self/fd/1 /var/log/apache2/error.log && \
  ln -sf /proc/self/fd/1 /var/log/opencpu/apache_access.log && \
  ln -sf /proc/self/fd/1 /var/log/opencpu/apache_error.log

# Set opencpu password so that we can login
RUN \
  echo "opencpu:opencpu" | chpasswd

# Apache ports
EXPOSE 80
EXPOSE 443
EXPOSE 8004

# Start non-daemonized webserver
CMD /usr/lib/rstudio-server/bin/rserver && apachectl -DFOREGROUND



# nuke cache dirs before installing pkgs; tip from Dirk E fixes broken img
RUN  rm -f /var/lib/dpkg/available && rm -rf  /var/cache/apt/*


RUN apt-get update && \
    apt-get -y  install --fix-missing gdb libxml2-dev python-pip libz-dev libmariadb-client-lgpl-dev
    # valgrind


RUN pip install awscli


ADD install.R /tmp/


RUN R -f /tmp/install.R && \
    echo "library(BiocInstaller)" > $HOME/.Rprofile