Dockerfile

FROM ubuntu:xenial

MAINTAINER Kristian Peters <kpeters@ipb-halle.de>

LABEL Description="MetFamily helps identifying metabolites and groups them into metabolite clusters (a.k.a. families)."



# Environment variables
ENV METFAMILY_BRANCH="master"
ENV PATH /usr/lib/rstudio-server/bin/:$PATH
ENV PACK_R="cba colourpicker devtools DT FactoMineR htmltools Matrix matrixStats plotrix rCharts rmarkdown shiny shinyBS shinyjs squash stringi tools"
ENV PACK_R="cba colourpicker devtools DT htmltools Matrix matrixStats plotrix rCharts rmarkdown shiny shinyBS shinyjs squash stringi tools"
ENV PACK_BIOC="mzR pcaMethods xcms"
ENV PACK_GITHUB=""

# Add cran R backport
RUN apt-get -y update
RUN apt-get -y install apt-transport-https
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
RUN echo "deb https://cran.uni-muenster.de/bin/linux/ubuntu xenial/" >> /etc/apt/sources.list

# Update & upgrade sources
RUN apt-get -y update
RUN apt-get -y dist-upgrade

# Install supervisord
RUN apt-get -y install supervisor

# Install r related packages
RUN apt-get -y install texlive-binaries r-base

# Install libraries needed for bioconductor
RUN apt-get -y install netcdf-bin libnetcdf-dev libdigest-sha-perl

# Install development files needed
RUN apt-get -y install git python xorg-dev libglu1-mesa-dev freeglut3-dev libgomp1 libxml2-dev gcc g++ libgfortran-4.8-dev libcurl4-gnutls-dev cmake wget ed libssl-dev gdebi-core

# Clean up
RUN apt-get -y clean && apt-get -y autoremove && rm -rf /var/lib/{cache,log}/ /tmp/* /var/tmp/*

# Install R packages
RUN for PACK in $PACK_R; do R -e "install.packages(\"$PACK\", repos='https://cran.r-project.org/')"; done

# Install Bioconductor packages
RUN R -e "source('https://bioconductor.org/biocLite.R'); biocLite(\"BiocInstaller\", dep=TRUE, ask=FALSE)"
RUN for PACK in $PACK_BIOC; do R -e "library(BiocInstaller); biocLite(\"$PACK\", ask=FALSE)"; done

# Install other R packages from source
#RUN for PACK in $PACK_GITHUB; do R -e "library('devtools'); install_github(\"$PACK\")"; done

# Install and configure shiny-server
WORKDIR /usr/src
RUN git clone https://github.com/rstudio/shiny-server.git
WORKDIR /usr/src/shiny-server
RUN mkdir tmp
WORKDIR /usr/src/shiny-server/tmp
RUN ../external/node/install-node.sh
RUN DIR=`pwd`; PATH=$DIR/../bin:$PATH; PYTHON=`which python`; cmake -DCMAKE_INSTALL_PREFIX=/usr/local -DPYTHON="$PYTHON" ../ && make && mkdir ../build && (cd .. && ./bin/npm --python="$PYTHON" rebuild)
RUN DIR=`pwd`; PATH=$DIR/../bin:$PATH; PYTHON=`which python`; (cd .. && ./bin/npm --python="$PYTHON" install && ./bin/node ./ext/node/lib/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js --python="$PYTHON" rebuild)
RUN make install
RUN ln -s /usr/local/shiny-server/bin/shiny-server /usr/bin/shiny-server
RUN useradd -r -m shiny
RUN mkdir -p /var/log/shiny-server
RUN mkdir -p /srv/shiny-server
RUN mkdir -p /var/lib/shiny-server
RUN chown -R shiny:shiny /var/log/shiny-server
RUN chown -R shiny:shiny /srv/shiny-server
RUN mkdir -p /etc/shiny-server
RUN wget https://raw.github.com/rstudio/shiny-server/master/config/upstart/shiny-server.conf -O /etc/init/shiny-server.conf
RUN cp -r /usr/src/shiny-server/samples/* /srv/shiny-server/
RUN wget https://raw.githubusercontent.com/rstudio/shiny-server/master/config/default.config -O /etc/shiny-server/shiny-server.conf

# Configure supervisor
ADD supervisord.conf /etc/supervisor/conf.d/supervisord.conf
RUN mkdir -p /var/log/supervisor
RUN chmod 777 -R /var/log/supervisor

# Using official github repository
RUN mv /srv/shiny-server /srv/shiny-server_orig
WORKDIR /srv
RUN git clone -b $METFAMILY_BRANCH https://github.com/ipb-halle/MetFamily
RUN mv MetFamily shiny-server

# Expose port
EXPOSE 3838

# Define Entry point script
WORKDIR /
#ENTRYPOINT ["/usr/bin/shiny-server","--pidfile=/var/run/shiny-server.pid"]
CMD ["/usr/bin/supervisord", "-c", "/etc/supervisor/conf.d/supervisord.conf"]