Singularity RStudio Server

The Image is based on the Ubuntu 22.04 (R 4.3.2), see ./singularity/rstudio_server/recipe-4-3-2.def for details

First step

You need to clone this repo. Go to:

$ cd singularity/

Second step (Option 1): Download the image file:

https://zenodo.org/records/14732727

Note: There you will also find all the R packages used for the single cell analyses.

Second step (Option 2): create the singularity image yourself:

$ sudo singularity build singularity-rstudio-4-3-2.sif recipe-4-3-2.def

Note: The image must be created in singularity/, as it includes the file singularity/rstudio_auth.sh, which is required when building the image

Third step (config and run)

The following adjustments must be made in the run.sh file:

• Set a port (variable RSTUDIO_PORT) Default: 8072
• Set a path for the log files (variable TMPDIR) Default: "/home/$USER/RStudio-Server-Files/"
• The variable RSTUDIO_PASSWORD can be set to a password of your choice. Default: "password"
• For parameter auth-pam-helper and rsession-config-file in run.sh: Set path to this folder.

Furthermore, set your R library path in ./singularity/rsession.conf. I recommend to create a new folder. It can lead to conflicts when folders with libraries of another R version are used.

Now run the following :

$ bash run.sh run singularity-rstudio-4-3-2.sif

You can reach RStudio Server via your webbrowser (e.g. localhost:8072/auth-sign-in). Use the port that you have specified in the variable RSTUDIO_PORT. You can log in with your current user name and password you set in RSTUDIO_PASSWORD.