Dockerfile

FROM rocker/shiny:latest
MAINTAINER Matthias Doering <mdoering@mpi-inf.mpg.de>
# R library dependencies considered in this dockerfile:
    #shinyjs, cshapes, countrycode, Biostrings, XML,, scales, gplots, reshape2, seqinr, IRanges, ggplot2, plyr, stringdist, stringr, doParallel, gtools, RColorBrewer, sets, DECIPHER, digest, shiny, DT, shinyBS, lpSolve,lpSolveAPI
# Python dependencies considered:
    # selenium
#install system packages
# libxml2 (required by R XML library), java runtime environment (required by MELTING), libssl-dev/unstable required by openssl package, libgsl0ldbl: required for viennaRNA,
# python-pip is necessary to install selenium for python (retrieval of template seqs)
# ensure that apt-get update works 
# pandoc (rmarkdown reports) requires latex for PDF output
# libmysqlclient-dev: required for RMySQL pkg
RUN rm -rf /var/lib/apt/lists/*
# changes: libssl-dev/unstable to libssl-dev because unstable not found (maybe need to change sources?)
# libmysqlclient-dev -> default-libmysqlclient-dev, libgslcblas0 -> libgsl0-dev
RUN apt-get update && apt-get install -y libfontconfig1 libxml2-dev default-jre libssl-dev libv8-dev libgsl0-dev python-pip pandoc texlive texlive-latex-extra default-libmysqlclient-dev
#    && rm -rf /var/lib/apt/lists/*
RUN pip install selenium
WORKDIR /srv/
RUN mkdir primer_design
ADD . primer_design
# install openPrimeR package to install all the dependencies of the tool
RUN Rscript primer_design/src/install.R FALSE TRUE
#update shiny server conf and configure it to run the primer design tool in single app mode
ADD shiny-server.conf /etc/shiny-server/shiny-server.conf
COPY .docker_bashrc /home/shiny/.bashrc
WORKDIR /srv/primer_design