greatly simplify Dockerfile

Dockerfile

@@ -1,91 +1,30 @@
-FROM ubuntu:xenial
+FROM rocker/shiny:latest
 
 MAINTAINER Kristian Peters <[email protected]>
 
 LABEL Description="MetFamily helps identifying metabolites and groups them into metabolite clusters (a.k.a. families)."
 
+RUN apt-get -y update && apt-get -y install \
+  netcdf-bin libnetcdf-dev libdigest-sha-perl \
+  xorg-dev libglu1-mesa-dev freeglut3-dev libgomp1 libxml2-dev gcc g++ libcurl4-gnutls-dev libssl-dev gdebi-core
 
+ADD binder/install.R /tmp
 
-# 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="BiocManager cba colourpicker devtools DT FactoMineR 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
+RUN for PACK in $PACK_BIOC; do R -e "BiocManager::install("\"$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
+#RUN R -e "source('/tmp/install.R')"
 
-# 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"]
+ADD . /srv/shiny-server/