Skip to content
Permalink
8fec4e7033
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
Go to file
 
 
Cannot retrieve contributors at this time
82 lines (64 sloc) 3.03 KB
# Pulls debian:latest from dockerhub
FROM debian
# Dockerfile questions go to
MAINTAINER C. Kuenne / MPI-BN / Bioinformatics / 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 && \
RUN wget https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.9.923-amd64.deb && \
gdebi -n shiny-server-1.5.9.923-amd64.deb && \
rm /srv/shiny-server/index.html && \
rm -rf /srv/shiny-server/sample-apps
#install shinythemes
RUN Rscript -e 'install.packages("shinythemes", repos="http://cran.wustl.edu/")'
#install shinyBS
RUN Rscript -e 'install.packages("shinyBS", repos="http://cran.wustl.edu/")'
#install old mvtnorm package (1.0-8), because the current 1.0-10 needs r 3.5 (current debian r is 3.3)
RUN Rscript -e 'devtools::install_version(repos="http://cran.wustl.edu/", package = "mvtnorm", version = "1.0-8")'
#Install WILSON
RUN Rscript -e 'devtools::install_github(repo = "loosolab/wilson", host="github.molgen.mpg.de/api/v3", auth_token = NULL, upgrade = "never")'
#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"]