Building an RStudio Singularity Container

RStudio Recommended Example

Initial Setup

mkdir rstudio_container
cd rstudio_container
# 
mkdir -p run var-lib-rstudio-server
printf 'provider=sqlite\ndirectory=/var/lib/rstudio-server\n' > database.conf
mkdir home

Add in your preferences:

RStudio stores your user preferences in rstudio-prefs.json. This file is in AppData/Roaming/RStudio on windows and ~/.config/rstudio on OSX/Linux.

mkdir ide_settings

Copy this file to ide_settings. It should look similar to this:

{
    "save_workspace": "never",
    "always_save_history": false,
    "reuse_sessions_for_project_links": true,
    "posix_terminal_shell": "bash",
    "initial_working_directory": "~",
    "panes": {
        "quadrants": [
            "Source",
            "TabSet1",
            "Console",
            "TabSet2"
        ],
        "tabSet1": [
            "Environment",
            "History",
            "Connections",
            "Build",
            "VCS",
            "Tutorial",
            "Presentation"
        ],
        "tabSet2": [
            "Files",
            "Plots",
            "Packages",
            "Help",
            "Viewer",
            "Presentations"
        ],
        "hiddenTabSet": [],
        "console_left_on_top": false,
        "console_right_on_top": true,
        "additional_source_columns": 0
    },
    "editor_theme": "Clouds Midnight"
}

Link to data you want to use:

ln -s /mnt/c/Users/drk8b9/Documents/LabProtocols/

(links can be removed with unlink [link name])

Build the singularity container

sudo singularity pull docker://rocker/rstudio:4.2 Once this is complete there should be a container file present: rstudio_4.2.sif.

(for customization construct a .def flie)

refer to the Rocker Project for more details on the available containers.

Running the container

To make use of the we need to run the container which will setup the path we need to bind our preferences to.

singularity exec \
  --bind run:/run \
  --bind var-lib-rstudio-server:/var/lib/rstudio-server \
  --bind database.conf:/etc/rstudio/database.conf \
  --bind home:/home \
  rstudio_4.2.sif \
  /usr/lib/rstudio-server/bin/rserver \
  --www-address=127.0.0.1 \
  --www-port=8700 \
  --server-user=rstudio
  
# note the arguments under --bind can be passed in on one line with ',' separating them. They are included separately to increase readability.

Press ctrl+c to exit the container. Now this container can be run with --bind ide_settings:/home/rstudio/.config/rstudio/ \ to use preferred settings.

Using the container

singularity exec \
  --bind run:/run \
  --bind var-lib-rstudio-server:/var/lib/rstudio-server \
  --bind database.conf:/etc/rstudio/database.conf \
  --bind home:/home \
  --bind LabProtocols:/home/rstudio/LabProtocols \
  --bind ide_settings:/home/rstudio/.config/rstudio/ \
  rstudio_4.2.sif \
  /usr/lib/rstudio-server/bin/rserver \
  --www-address=127.0.0.1 \
  --www-port=8700 \
  --server-user=rstudio
  
# note, you can also bind a folder or file by it's full path. For me on WSL this would be
# --bind /mnt/c/Users/drk8b9/Documents/LabProtocols:/home/rstudio/LabProtocols \

Login with defaults: “rstudio” and “rstudio”.