RStudio
RStudio is an integrated development environment for R. On the DSRI it runs as a container based on Rocker RStudio tidyverse images (Debian), with sudo privileges so you can install anything you need using pip, apt, or R's install.packages().
Deploy
Find the RStudio template in the DSRI Catalog (make sure the Templates checkbox is checked) and instantiate it. You will need to set a password to access the UI. The username will always be root.
If you need Bioconductor packages for genomics or single-cell RNA sequencing analysis, use the Bioconductor with RStudio template instead. It includes Bioconductor 3.21 with R 4.5.2 pre-installed. Everything else works the same way.
Persistent storage
A persistent volume is automatically created at /root/persistent. Data stored in this folder survives pod restarts. You can find it in the DSRI web UI under Administrator view > Storage > Persistent Volume Claims.
Use git
The fastest way to get started is to use git from the terminal. For example, to clone a repository:
git clone https://github.com/your-org/your-repo.git
Before pushing to GitHub or GitLab, configure your username and email:
git config --global user.name "Jean Dupont"
git config --global user.email jeandupont@gmail.com
To save your password for 15 minutes:
git config credential.helper cache
Or store it in a plain text file:
git config --global credential.helper 'store --file ~/.git-credentials'
We recommend using SSH instead of HTTPS where possible. See GitHub's guide on generating SSH keys.
You can also enable the built-in Git integration in RStudio - see the RStudio Git documentation for instructions.
Run R jobs
To run a standalone R job on the DSRI, see the dsri-demo repository for resources and instructions.
To run chunks of R code as background jobs directly from RStudio, see the job package.