RStudio deployment for fun and profit

Overview

Teaching: 0 min
Exercises: 30 min

Questions

Objectives

Run an R workflow through both the terminal and RStudio using containers

Deploy a customised RStudio container for bioinformatics

RStudio example

R is a popular language in several domains of science, particularly because of its statistical packages. It often requires installing a large number of dependencies, and installing these on an HPC system can be tedious.

Instead we can use an R container to simplify the process.

Rocker

The group Rocker has published a large number of R images we can use, including an Rstudio image. To begin, we’ll pull a Tidyverse container image (contains R, RStudio, data science packages):

$ docker pull rocker/tidyverse:3.5

Running a scripted R workflow on the shell

Let us cd to the 06_rstudio demo directory:

$ cd <top-level>/demos/06_rstudio

We are going to use an example example that has been derived from the workshop Programming with R by the Software Carpentry. In particular, their Episode 5 is the source for the dataset and the R script file; the latter has been adapted for this workshop.

Now, let us run the R script using the R container we pulled; we’re going to compute average values in this example:

$ docker run -v `pwd`:/data -w /data rocker/tidyverse:3.5 Rscript readings-density.R --mean inflammation-density.png data/inflammation-*.csv

45
425
1
[..]
875
025
9
Saving 7 x 7 in image

The analysis outputs a plot in a picture file, inflammation-density.png, that can be opened and visualised.

Using an RStudio web server to run the workflow

Let us setup an RStudio web server using Docker, by using the following command:

$ docker run --rm -d -p 80:8787 --name=rstudio -v `pwd`:/home/rstudio -e PASSWORD=<Pick your password> rocker/tidyverse:3.5

Here we’re opening up the container port 8787 and mapping it to the host port 80 so we can access the Rtudio server remotely. Note you need to store a password in a variable; it will be required below for the web login. Also, we are mapping the current directory into home/rstudio in the container; this is the default RStudio working directory in Rocker containers.

You just need to open a web browser and point it to localhost if you are running Docker on your machine, or <Your VM's IP Address> if you are running on a cloud service.

You should see a prompt for credentials, with user defaulting to rstudio, and password..

Now you can run the same analysis from the RStudio console:

> source("readings-density.R")

This time the output plot is saved in the file interactive.png.

Once you’re done, stop the container with:

$ docker stop rstudio

Customised RStudio images

The above example only provides a bare-bones RStudio image, but now we want to actually use some R packages. The following example is based on a bioinformatics workshop at OzSingleCell2018. We’ll use their data for our Docker/Rstudio example.

To begin, let’s cd to the 06_rstudio_bio demo directory, where a trimmed down repo with their data has been created for this tutorial, and then uncompress a required input file:

$ cd <top-level>/demos/06_rstudio_bio
$ gunzip data/matrix.mtx.gz

For this example, we’ll use an RStudio image thas has already been built. R images can take a while to build sometimes, depending on the number of packages and dependencies you’re installing. The Dockerfile used here is included, and we’ll briefly comment through it.

FROM rocker/tidyverse:3.5

RUN apt-get update -qq && apt-get -y --no-install-recommends install \
      autoconf \
      automake \
      g++ \
      gcc \
      gfortran \
      make \
      && apt-get clean all \
      && rm -rf /var/lib/apt/lists/*

RUN mkdir -p $HOME/.R
COPY Makevars /root/.R/Makevars

RUN Rscript -e "library('devtools')" \
      -e "install_github('Rdatatable/data.table', build_vignettes=FALSE)" \
      -e "install.packages('reshape2')" \
      -e "install.packages('fields')" \
      -e "install.packages('ggbeeswarm')" \
      -e "install.packages('gridExtra')" \
      -e "install.packages('dynamicTreeCut')" \
      -e "install.packages('DEoptimR')" \
      -e "install.packages('http://cran.r-project.org/src/contrib/Archive/robustbase/robustbase_0.90-2.tar.gz', repos=NULL, type='source')" \
      -e "install.packages('dendextend')" \
      -e "install.packages('RColorBrewer')" \
      -e "install.packages('locfit')" \
      -e "install.packages('KernSmooth')" \
      -e "install.packages('BiocManager')" \
      -e "source('http://bioconductor.org/biocLite.R')" \
      -e "biocLite('Biobase')" \
      -e "biocLite('BioGenerics')" \
      -e "biocLite('BiocParallel')" \
      -e "biocLite('SingleCellExperiment')" \
      -e "biocLite('GenomeInfoDb')" \
      -e "biocLite('GenomeInfgoDbData')" \
      -e "biocLite('DESeq')" \
      -e "biocLite('DESeq2')" \
      -e "BiocManager::install(c('scater', 'scran'))" \
      -e "library('devtools')" \
      -e "install_github('IMB-Computational-Genomics-Lab/ascend', ref = 'devel')" \
      && rm -rf /tmp/downloaded_packages

The first line, FROM, specifies a base image to use. We could build up a full R image from scratch, but why waste the time. We can use Rocker’s pre-built image to start with and simplify our lives.

RUN apt-get update is installing some packages we’ll need via Ubuntu’s package manager. Really all we’re installing here are compilers.

The next section adds some flags and options we want to use when building R packages, by copying a file from the build context, Makvevars.

The last section is the main R package installation section. Here we run several different installation methods:

install.packages() is R’s standard method for installing packages from CRAN. We also install the robustbase package from source here.
biocLite() is Bioconductor’s method for installing packages
BiocManager is a CRAN package for installing bioinformatics software
install_github() is method for installing R packages from GitHub.

We’ll skip building this image for now, and just pull and use a prebuilt image:

$ docker pull bskjerven/oz_sc:latest

Now let us setup an RStudio server based on it:

$ docker run --rm -d -p 80:8787 --name=rstudio -v `pwd`:/home/rstudio -e PASSWORD=<Pick your password> bskjerven/oz_sc:latest

Shortly after this starts, open a web browser and go to localhost if you are running Docker on your machine, or <Your VM's IP Address> if you are running on a cloud service. You should see an Rstudio login, and we’ve set the username to rstudio and password..

Once logged in, you type (note this is the R shell):

> source('data/SC_script.r')

to run the tutorial (it may take a few minutes). We can refer to the OzSingleCell2018 repo for details on each step.

To stop your Rstudio image, simply type:

$ docker stop rstudio

Key Points

Containers are great way to manage R workflows. You likely still want to have a local installation of R/Rstudio for some testing, but if you have set workflows, you can use containers to manage them. You can also provide Rstudio servers for collaborators

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Intro to Docker (Pawsey Centre)

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