IDE Container: RStudio Server, Shiny Server, and More

Introduction

The goal of this sevenbridges/sevenbridges-r Docker image is to provide

  • Seven Bridges SDK environment that includes
    • Seven Bridges Platform command line uploader
    • Seven Bridges command line tools
    • R package sevenbridges with essential dependencies
  • RStudio Server
  • Shiny Server

Docker container

Build container locally

The Dockerfile is included with the package in inst/docker folder.

Here is the current content of Dockerfile:

fl <- system.file("docker/sevenbridges/", "Dockerfile", package = "sevenbridges")
cat(readLines(fl), sep = "\n")
FROM rocker/tidyverse

LABEL maintainer="[email protected]"

## Install common dependencies
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 update \
    && apt-get install -y apt-transport-https ca-certificates gnupg2 software-properties-common \
    && curl -fsSL https://download.docker.com/linux/debian/gpg | sudo apt-key add - \
    && apt-key fingerprint 0EBFCD88 \
    && add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/debian $(lsb_release -cs) stable" \
    && apt-get update -y \
    && apt-get install -y docker-ce

##################
# sevenbridges-r #
##################

# Install from GitHub instead of Bioconductor for the latest version
RUN Rscript -e "install.packages('BiocManager');\
    devtools::install_github('sbg/sevenbridges-r', repos = BiocManager::repositories(), build_vignettes = FALSE, dependencies = TRUE)"

#####################
# Seven Bridges SDK #
#####################

## Install SBG Rabix
RUN wget https://github.com/rabix/bunny/releases/download/v1.0.5-1/rabix-1.0.5.tar.gz \
    && tar -zvxf rabix-1.0.5.tar.gz \
    && ln -s  /rabix-cli-1.0.5/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 and packrat
RUN Rscript -e "install.packages(c('liftr', 'packrat'), repos = 'https://cloud.r-project.org/')"

## (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://cloud.r-project.org/')"

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"]

You can simply build it locally, enter folder which contain that Dockerfile, in this case, it is under inst/docker/sevenbridges

docker build -t sevenbridges/sevenbridges-r .

Pull from Docker Hub

A hook is added to build the Docker image automatically from the sevenbridges-r GitHub repository. It is automatically built on Docker Hub. You can directly use this image sevenbridges/sevenbridges-r. Everytime a push is made in the GitHub repo, the Docker container is re-built.

Launch RStudio Server from Docker container

For example, you can ssh into your AWS instance, here I suppose you already have Docker installed, and pull the image

docker pull sevenbridges/sevenbridges-r

To launch sevenbridges RStudio Server image, I recommend you read this tutorial

Or following the quick instruction here

docker run -d -p 8787:8787 sevenbridges/sevenbridges-r
docker run -d -p 8787:8787 -e USER=<username> -e PASSWORD=<password> rocker/rstudio

You will be able to access the RStudio in the browser by something like

http://<your_ip_address>:8787

Sometimes you want to add more users, to add users

## Enter the container
docker exec -it <container-id> bash
## Interactively input password and everything else
adduser <username>

Launch both RStudio Server and Shiny Server from the same Docker container

Sometimes it is very conventient to launch both RStudio Server and Shiny Server from a singel container and your users can manage to using RStudio Server and publish Shiny apps at the same time in the same container. To do so, just pull the same image and launch them at different port.

docker run  -d -p 8787:8787 -p 3838:3838 --name rstudio_shiny_server sevenbridges/sevenbridges-r

To mount file system you need to use --privileged with fuse.

docker run  --privileged -d -p 8787:8787 -p 3838:3838 --name rstudio_shiny_server sevenbridges/sevenbridges-r

check out the ip from docker machine if you are on mac os.

docker-machine ip default

In your browser, http://<url>:8787/ for RStudio Server, for example, if 192.168.99.100 is what returned, visit http://192.168.99.100:8787/ for RStudio Server.

For Shiny Server, per user app is hosted http://<url>:3838/users/<username of rstudio>/<app_dir>, for example, for user rstudio (a default user) and an app called 01_hello, it will be http://<url>:3838/users/rstudio/01_hello/. To develop your Shiny app from RStudio Server, you can log into your RStudio Server with your username, and create a fold at home folder called ~/ShinyApps and develop Shiny apps under that folder, for example, you can create an app called 02_text at ~/ShinyApps/02_text/.

Let’s try this, please log into your RStudio at http://<url>:8787 now, then try to copy some example over to your home folder under ~/ShinyApps/

dir.create("~/ShinyApps")
file.copy(
  "/usr/local/lib/R/site-library/shiny/examples/01_hello/",
  "~/ShinyApps/", recursive = TRUE
)

If you logged in with the username rstudio, then visit http://192.168.99.100:3838/rstudio/01_hello you should be able to see the hello example.

Note: Generic Shiny apps can also be hosted http://<url>:3838/ or for particular app, http://<url>:3838/<app_dir> and inside the Docker container, it is hosted under /srv/shiny-server/.