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RStudio on Linux server

How to make the environment

  1. Make an environment with apptainer, it is the only program needed.
  2. Create a directory $CONDA_PREFIX/rstudio-images
  3. Download correct images: apptainer pull docker://bioconductor/bioconductor_docker:devel
  4. Copy the run.sh script to $CONDA_PREFIX/bin as rstudio-web, make sure it is executable.
  5. Copy the message.sh script to $cONDA_PREFIX/etc/conda/activate.d/, make the directory if not exist.

Note: Make sure your image have development tools for building some R packages.

What will happen on user side

RStudio Execution

  • The RStudio server runs within an Apptainer container
  • When launched, you'll receive:
    • A randomly generated port number
    • A randomly generated password for your session
    • SSH tunneling instructions for remote access
    • Direct URL for local access
  • You can specify CPU cores and custom port numbers with options like --cpus and --port

Temporary Files in Home Directory

  • Two temporary files will be created in your home directory:
    • custom_rsession.conf: Configuration for your R session
    • A symlink to /vol/local at ~/vol-local-entry-RSTUDIO
  • These files are automatically removed when your session ends

R Package Installation

  • R packages are installed to /vol/local/$USER/Rstudio/$R_VERSION
  • This location persists between sessions
  • The R version is automatically detected from the container
  • Using this location keeps your packages organized by R version

R Session Workspace

  • Your R workspace defaults to /vol/local/$USER/RStudio/workspace
  • This prevents clutter in your home directory
  • The .RData and history files are stored in this location
  • This directory is created automatically if it doesn't exist

CPU Core Allocation

  • By default, your session uses all available CPU cores
  • You can limit CPU usage with --cpus N to use N cores
  • You can specify exact cores with --cpus 0,2,4 syntax
  • The system manages core allocations to prevent conflicts between users
  • Allocated cores are automatically released when your session ends

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