ctmrbio/rstudio_singularity

Run Rstudio with Singularity

rstudio_singularity

Run Rstudio with Singularity

Based on documentation here: https://rocker-project.org/use/singularity.html

Run RStudio on CTMR Gandalf

Run RStudio server in Singularity.

usage: launch_rstudio [-h] -p PORT [-P PASSWORD] [-i IMAGE]

options:
-i IMAGE      RStudio Docker IMAGE to use (default: /ceph/apps/rstudio/rocker_tidyverse-4.3.3.sif
-P PASSWORD   Set the PASSWORD for logging into RStudio (default: secret).
-p PORT       PORT used to access RStudio, required.
-h            Print this help.

Access via browser at:
   http://localhost:PORT

Login with:
   user: USERNAME
   pass: secret  (change with -P PASSWORD)

On CTMR Gandalf, this script is installed and available in every user's PATH as ctmr-launch_rstudio.sh. Run the following command to launch RStudio in Singularity on PORT:

ctmr-launch_rstudio.sh -p PORT

Note that specifying a PORT is required, pick your favorite port that no one else uses.

The /ceph file system is bound at /ceph inside the running container. If you are running this on another system than CTMR Gandalf, remove this from the --bind argument to Singularity.

Custom RStudio Singularity image

This repo contains a customized Singularity deffile rstudio.Singularityto create a new image containing additional system libraries/packages required for some R packages. It can be built with:

sudo singularity build ctmr_rocker_tidyverse-4.3.3-2.0.sif rstudio.Singularity