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README.md

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To use this notebook

  1. Go to ood.ccv.brown.edu (you will need an Oscar account).
  2. Go to 'Clusters' in the blue menu bar at the top and click the drop-down that says '>_OSCAR Shell Access'
  3. Go to your home folder (cd ~)
  4. Git clone the repo (`git clone https://github.com/compbiocore/ccv_bootcamp_annotations.git`)
  5. Go back to ood.ccv.brown.edu and look under Interactive Apps in the blue menu bar and click on RStudio on Singularity under Expert GUIs.

Fill in the fields as follows:

  • Account: leave blank

  • Partition: leave blank

  • Number of hours: 24

  • Num Cores: 4

  • Memory: 15

  • Singularity Container Path:/oscar/data/shared/databases/workshops/bootcamp_2024/ngs_counts/ngscounts.sif

  • Package install Path: leave blank

  • Path for R Executable: ~/scratch

  • R Module: leave blank

  • Additional Data Path: leave blank

  • Reservation: leave blank

I added many of you to the reservation, but not all of you, so you might need to leave the Reservation field blank as well. Once your job starts, click the button to connect to session. At the top of the screen you'll see a menu bar that starts with 'file', click on 'file' and 'open file' and open the notebooks/index.qmd file in the repo you cloned.