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Therkildsen Lab User-Guide
Using the HPC
Using R on the server

Using R on the server

The instructions on this page are specific to doing things on the server, not your local machine.

Running RStudio on the server

  1. Run this command to start RStudio server
/programs/rstudio_server/rstudio_start
  1. From a browser on your laptop/desktop computer, go to http://cbsunt246.biohpc.cornell.edu:8015
  • Sometimes, you might need to reshresh the page once. Log in using your biohpc username and password
  1. If you want to stop the RStudio Server, using this command:
/programs/rstudio_server/rstudio_stop

Avoid re-plotting figures when knitting an Rmd

You can set eval=F in the code block, run it manually, and save the figure to a file. Then, you can start a new code block, set eval=T, and use include_graphics("path_to_the_figure") to show the figure. Note that if you are knitting to a GitHub formatted md file, the figure needs to be pushed to GitHub as well for it to show up on the GitHub site.

Using Positron on the server

Positron is an data science IDE developed by Posit, the developers of RStudio. It’s designed to be the successor to the RStudio software by being a flexible, user-friendly workspace. For more info, check out this video for a full breakdown of Positron’s features. Positron is effectively a reskinned version of Visual Studio Code but with some extra R-specific features, such as customizable plotting and the ability to see all environment variables and dataframes. Beyond R, Positron also supports Python interpreters and has a seamless GitHub integration. Like VS Code, Positron features a marketplace of useful extensions for a variety of tasks.

Positron is currently in beta, meaning that some features remain in-progress or missing and you may run into bugs. However, you can still install it via its GitHub Releases page. To get it working on our server, you will first need to go into the Settings (File > Preferences > Settings) and search for Kallichore, and check Kallichore Supervisor: Enable. You will then need to connect via ssh by hitting Ctrl + Shift + P on your keyboard and typing in Remote-SSH: Connect to Host. You will be prompted to enter your ssh host address, which should be yournetid@cbsunt246.biohpc.cornell.edu. A new window should open, and you will need to enter your BioHPC password. You can then select your working directory by going to the Explorer panel and selecting Open Folder and pointing to your desired working directory.

For more information on customizing Positron, check out this link, which is a bit outdated but contains some useful info on settings and extensions you can implement for a good experience.

Snakemake + SLURM