IDE container: Rstudio and Shiny server and more

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')

Warning in readLines(fl): incomplete final line found on '/tmp/RtmpONvHXF/
Rinst62fe424537de/sevenbridges/docker/sevenbridges//Dockerfile'

FROM rocker/rstudio-daily:verse
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 \
    libcairo2-dev \
    libxt-dev \
    unp \
    emacs \
    supervisor 
    
## install docker
RUN apt-get install -y apt-transport-https ca-certificates \
    && apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D \
    && echo "deb https://apt.dockerproject.org/repo debian-stretch main" > /etc/apt/sources.list.d/docker.list \
    && echo "//APT::Default-Release \"testing\";" > /etc/apt/apt.conf.d/default   \
    && apt-get update \
    && apt-get install -y docker-engine



####################
### addin
###################

RUN R -e "install.packages(c('rstudioapi', 'miniUI'), type = 'source'); "


##################
### Bioc
#################

## install from github instead of bioc 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)'




##################
### SBG
#################

## 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 SBG rabix
RUN wget https://github.com/rabix/bunny/releases/download/v0.1.0-alpha/rabix-0.1.1-alpha.tar.gz \
    && tar -zvxf rabix-0.1.1-alpha.tar.gz \
    && ln -s  /rabix-0.1.1-alpha/rabix.sh /usr/local/bin/rabix.sh


## install SBG 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

## start insert command line interface and report template needed
ADD src/runif.R /usr/local/bin/
RUN mkdir /report/ 
ADD report/report.Rmd /report/






## liftr
RUN R -e "devtools::install_github('road2stat/liftr', ref = 'devel')"
RUN R -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
###################

## thanks to official shiny docker file

# Download and install libssl 0.9.8
RUN wget --no-verbose http://ftp.us.debian.org/debian/pool/main/o/openssl/libssl1.0.2-dbg_1.0.2h-1_amd64.deb && \
    dpkg -i libssl1.0.2-dbg_1.0.2h-1_amd64.deb && \
    rm -f libssl1.0.2-dbg_1.0.2h-1_amd64.deb

# 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 ss-latest.deb && \
    gdebi -n ss-latest.deb && \
    rm -f version.txt ss-latest.deb

RUN R -e "install.packages(c('shiny', 'rmarkdown'), repos='https://cran.rstudio.com/')"

RUN R -e "devtools::install_github('rstudio/addinexamples', type = 'source')"

RUN R -e "devtools::install_github('rstudio/rsconnect')"

RUN R -e "devtools::install_github('rstudio/shinyapps')"

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
COPY src/shiny-server.conf  /etc/shiny-server/shiny-server.conf
COPY src/supervisord.conf /etc/supervisor/conf.d/supervisord.conf

## ~/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’s under inst/docker/sevenbridges

docker build -t tengfei/sevenbridges .

Pull from docker hub

A hook is added to build the docker image automatically from my github, it’s under inst/docker, it’s automatically build on my dockerhub page. you can directly use this tengfei/sevenbridges. Everytime a push is made in the github repos, 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 tengfei/sevenbridges

To launch sevenbridges Rstudio server image, I recommend you read this tutorial

Or following the quick instruction here

docker run -d -p 8787:8787 tengfei/sevenbridges
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 and Shiny server from same docker container

Sometimes it’s very conventient to launch both Rstudio and Shiny server from a singel container and your users can manage to using Rstudio 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 tengfei/sevenbridges

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.

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 login 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 login 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 are login as 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 app can also be hosted http://<url>:3838/ or for particular app, http://<url>:3838/<app_dir> and inside the docker container, it’s hosted under /srv/shiny-server/