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FROM rocker/tidyverse MAINTAINER "Tengfei Yin" yintengfei@gmail.com ## Install Docker (Docker in Docker) RUN apt-get update && apt-get install -y \ sudo \ gdebi-core \ pandoc \ pandoc-citeproc \ libcurl4-gnutls-dev \ curl \ libcairo2-dev \ libxt-dev \ unp \ emacs \ supervisor \ libfuse-dev \ gnupg # aufs-tools \ # cgroupfs-mount # RUN wget --no-verbose http://ftp.us.debian.org/debian/pool/main/l/lvm2/libdevmapper1.02.1_1.02.136-1_amd64.deb && \ # dpkg -i libdevmapper1.02.1_1.02.136-1_amd64.deb && \ # rm -f libdevmapper1.02.1_1.02.136-1_amd64.deb # RUN wget --no-verbose http://ftp.us.debian.org/debian/pool/main/libt/libtool/libltdl7_2.4.6-2_amd64.deb && \ # dpkg -i libltdl7_2.4.6-2_amd64.deb && \ # rm -f libltdl7_2.4.6-2_amd64.deb ## Install Docker RUN apt-get install -y apt-transport-https ca-certificates \ && apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D \ && echo "deb https://apt.dockerproject.org/repo debian-$(lsb_release -cs) main" > /etc/apt/sources.list.d/docker.list \ && echo "//APT::Default-Release \"testing\";" > /etc/apt/apt.conf.d/default \ && apt-cache policy docker-engine RUN apt-get update -y \ && apt-get upgrade -y \ && apt-get install -y docker-engine ################# # RStudio addin # ################# RUN Rscript -e "install.packages(c('rstudioapi', 'miniUI'), type = 'source');\ devtools::install_github('rstudio/addinexamples')" ################ # Bioconductor # ################ # Install from GitHub instead of Bioconductor for latest version RUN Rscript -e "source('http://bioconductor.org/biocLite.R');\ devtools::install_github('sbg/sevenbridges-r', build_vignettes = FALSE, repos = BiocInstaller::biocinstallRepos(), dependencies = TRUE)" # RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller);biocLite("sevenbridges", dep = TRUE)' ################# # Seven Bridges # ################# ## Install SBG Rabix RUN wget https://github.com/rabix/bunny/releases/download/v1.0.2/rabix-cli-1.0.2.tar.gz \ && tar -zvxf rabix-cli-1.0.2.tar.gz \ && ln -s /rabix-cli-1.0.2/rabix /usr/local/bin/rabix ## Install SBG Command line uploader # RUN wget https://igor.sbgenomics.com/sbg-uploader/sbg-uploader.tgz \ # && tar zxvf sbg-uploader.tgz -C / \ # && ln -s /sbg-uploader/bin/sbg-uploader.sh /usr/local/bin/sbg-uploader.sh ## Install CGC Command line uploader # RUN wget https://cgc.sbgenomics.com/cgc-uploader/cgc-uploader.tgz \ # && tar zxvf cgc-uploader.tgz -C / \ # && ln -s /cgc-uploader/bin/cgc-uploader.sh /usr/local/bin/cgc-uploader.sh ## Copy command line interface and report templates needed ADD src/runif.R /usr/local/bin/ RUN mkdir /report/ ADD report/report.Rmd /report/ ## Install liftr RUN Rscript -e "devtools::install_github('road2stat/liftr', ref = 'devel')" RUN Rscript -e "devtools::install_github('rstudio/packrat')" ## (because --deps TRUE can fail when packages are added/removed from CRAN) RUN rm -rf /var/lib/apt/lists/ \ && rm -rf /tmp/downloaded_packages/ /tmp/*.rds ################ # Shiny Server # ################ ## Thanks: rocker-org/shiny ## Download and install Shiny Server RUN wget --no-verbose https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/VERSION -O "version.txt" && \ VERSION=$(cat version.txt) && \ wget --no-verbose "https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/shiny-server-$VERSION-amd64.deb" -O shiny-server-latest.deb && \ gdebi -n shiny-server-latest.deb && \ rm -f version.txt shiny-server-latest.deb RUN Rscript -e "install.packages(c('shiny', 'rmarkdown', 'rsconnect'), repos = 'https://cran.rstudio.com/')" RUN cp -R /usr/local/lib/R/site-library/shiny/examples/* /srv/shiny-server/ RUN mkdir /home/rstudio/ShinyApps/ RUN cp -R /usr/local/lib/R/site-library/shiny/examples/* /home/rstudio/ShinyApps/ EXPOSE 3838 8787 # COPY src/shiny-server.sh /usr/bin/shiny-server.sh # RUN wget --no-verbos https://raw.githubusercontent.com/sbg/sevenbridges-r/master/inst/docker/sevenbridges/src/shiny-server.conf -P /etc/shiny-server/ # RUN wget --no-verbos https://raw.githubusercontent.com/sbg/sevenbridges-r/master/inst/docker/sevenbridges/src/supervisord.conf -P /etc/shiny-server/ COPY src/shiny-server.conf /etc/shiny-server/shiny-server.conf COPY src/supervisord.conf /etc/supervisor/conf.d/supervisord.conf ## set directory to `~/ShinyApps` # RUN yes | /opt/shiny-server/bin/deploy-example user-dirs # RUN cp -R /usr/local/lib/R/site-library/shiny/examples/* ~/ShinyApps/ CMD ["/usr/bin/supervisord", "-c", "/etc/supervisor/conf.d/supervisord.conf"] # CMD ["/init;/usr/bin/shiny-server.sh"] # CMD ["sh", "-c", "/usr/bin/shiny-server.sh;/init"]
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