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RStudio

Start RStudio

Start a RStudio container based on Rocker RStudio tidyverse images (debian), with sudo privileges to install anything you need (e.g. pip or apt packages)

You can start a container using the RStudio template in the Catalog web UI (make sure the Templates checkbox is checked)

Provide a few parameters, and Instantiate the template. The username will be rstudio, and the DSRI will automatically create a persistent volume to store data you will put in the /home/rstudio folder. You can find the persistent volumes in the DSRI web UI, go to the Administrator view > Storage > Persistent Volume Claims.

Deploy RStudio
Official image documentation

See the official Docker image documentation for more details about the container deployed.

Restricted RStudio with Shiny server

Start a RStudio application, with a complementary Shiny server, using a regular rstudio user, without sudo privileges.

Create the template in your project:

  • In the DSRI web UI, go to + Add, then click on YAML, add the content of the template-rstudio-shiny-restricted.yml file, and validate.

  • You can also do it using the terminal:

    oc apply -f https://raw.githubusercontent.com/MaastrichtU-IDS/dsri-documentation/master/applications/templates/restricted/template-rstudio-shiny-restricted.yml

Once the template has been created in your project, use the RStudio with Shiny server template in the OpenShift web UI catalog. It will automatically create a persistent storage for the data.

No sudo privileges

You will not have sudo privileges in the application.

Use Git in RStudio

The fastest way to get started is to use git from the terminal, for example to clone a git repository use git clone

You can also check how to enable Git integration in RStudio at https://support.rstudio.com/hc/en-us/articles/200532077

You can run this command to ask git to save your password for 15min:

git config credential.helper cache

Or store the password/token in a plain text file:

git config --global credential.helper 'store --file ~/.git-credentials'

Before pushing back to GitHub or GitLab, you will need to configure you username and email in the terminal:

git config --global user.name "Jean Dupont"
git config --global user.email jeandupont@gmail.com
Git tip

We recommend to use SSH instead of HTTPS connection when possible, checkout here how to generate SSH keys and use them with your GitHub account.

Run R jobs

You can visit this folder that gives all resources and instructions to explain how to run a standalone R job on the DSRI: https://github.com/MaastrichtU-IDS/dsri-demo/tree/main/r-job

If you want to run jobs directly from RStudio, checkout this package to run chunks of R code as jobs directly through RStudio: https://github.com/lindeloev/job