RStudio

Introduction

RStudio is an integrated development environment (IDE) for the R statistical computation and graphics system.

This is an RStudio IDE together with a plain R-base installation (see https://github.com/rocker-org/rocker/), repackaged by RCAC with an addition of a handful prerequisite libraries (libcurl, libopenssl, libxml2, libcairo2 and libXt) and their header files. It is intentionally separate from the biocontainers’ ‘r’ module for reasons of image size (700MB vs 360MB).

For more information, please check its | Docker hub: https://hub.docker.com/_/r-base and its home page: https://www.rstudio.com/products/rstudio/ and https://www.r-project.org/.

Versions

• 4.1.1

Commands

• R

• Rscript

• rstudio

Module

You can load the modules by:

module load biocontainers
module load r-studio

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run RStudio on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=r-studio
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers r-studio