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wilson-apps/docker/1.5.3/Dockerfile
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# Pulls debian:latest from dockerhub | |
FROM debian | |
# Dockerfile questions go to | |
MAINTAINER C. Kuenne / MPI-BN / Bioinformatics Core Unit / carsten.kuenne@mpi-bn.mpg.de | |
#Some basic packages, updates and cleanup | |
RUN apt-get -y update && apt-get -y upgrade && \ | |
apt-get -y install \ | |
r-base \ | |
wget \ | |
libnlopt-dev \ | |
libssl-dev \ | |
libxml2-dev \ | |
libcurl4-openssl-dev \ | |
git \ | |
procps \ | |
gdebi-core && \ | |
apt-get clean | |
#Installs DEVTOOLS | |
RUN Rscript -e "install.packages(c('devtools'), \ | |
repos='https://cran.rstudio.com/')" | |
#Installs BIOCONDUCTOR/BiocInstaller | |
RUN Rscript -e 'source("https://bioconductor.org/biocLite.R")' | |
#Install Shiny-Server | |
#RUN wget https://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.5.6.875-amd64.deb && \ | |
#gdebi -n shiny-server-1.5.6.875-amd64.deb && \ | |
RUN wget https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.7.907-amd64.deb && \ | |
gdebi -n shiny-server-1.5.7.907-amd64.deb && \ | |
rm /srv/shiny-server/index.html && \ | |
rm -rf /srv/shiny-server/sample-apps | |
#Install WILSON | |
RUN Rscript -e 'devtools::install_github(repo = "loosolab/wilson", host="github.molgen.mpg.de/api/v3")' | |
#Install stackdump | |
#RUN Rscript -e 'devtools::install_github(repo = "jcheng5/stackdump")' | |
#Install WILSON App | |
#RUN git clone -b stackdump https://github.molgen.mpg.de/loosolab/wilson-apps /srv/shiny-server/tmp && \ | |
RUN git clone https://github.molgen.mpg.de/loosolab/wilson-apps /srv/shiny-server/tmp && \ | |
cp -a /srv/shiny-server/tmp/wilson-basic/. /srv/shiny-server/ && \ | |
rm -rf /srv/shiny-server/tmp | |
#Install webshot/phantomjs to permit download of interactive plots with plot.ly | |
RUN Rscript -e 'install.packages("webshot", repos="http://cran.wustl.edu")' | |
RUN Rscript -e 'webshot::install_phantomjs()' | |
RUN cp /root/bin/phantomjs /usr/local/bin | |
EXPOSE 3838 | |
RUN rm -rf /srv/shiny-server/data && \ | |
mkdir /srv/shiny-server/data | |
#check current directory for the presence of clarion input files (*.se, *.clarion) -> include in container | |
#add pointless additional copy of entrypoint.sh because otherwise the building will fail if no clarion files exist (yuck!) | |
ADD entrypoint.sh *.se *.clarion /srv/shiny-server/data/ | |
RUN rm /srv/shiny-server/data/entrypoint.sh | |
ADD entrypoint.sh /usr/bin/entrypoint.sh | |
RUN chmod +x /usr/bin/entrypoint.sh | |
#switch shiny user uid to 1000 (previously docker user); set permissions | |
RUN usermod -u 1000 shiny && \ | |
chown -R shiny:shiny /srv/shiny-server/ && \ | |
mkdir -p /srv/shiny-server/logs && \ | |
chmod ugo+wrX /srv/shiny-server/logs | |
CMD ["/usr/bin/entrypoint.sh"] |