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Setup

Once you have an account and are connected to the VPN/Tufts Network, navigate to the OnDemand Website and log in with your tufts credentials. Once you are logged in you'll notice a few navigation options:

Click on Interactive Apps > RStudio Pax and you will see a form to fill out to request compute resources to use RStudio on the Tufts HPC cluster. We will fill out the form with the following entries:

  • Number of hours : 3
  • Number of cores : 1
  • Amount of memory : 8GB
  • R version : 4.0.0
  • Reservation for class, training, workshop : Bioinformatics Workshop---> NOTE: This reservation closed on Nov 9, 2022, use Default if running through the materials after that date.
  • Load Supporting Modules: boost/1.63.0-python3 java/1.8.0_60 gsl/2.6

Click Lauch and wait until your session is ready. Click Connect To RStudio Server, and you will notice a new window will pop up with RStudio.

Project Setup

We are going to create a new project to begin:

  1. Go to File > New Project
  2. New Directory
  3. New Project
  4. Create a name for your project (e.g. intro-to-proteomics)
  5. Create Project

File Organization

In our project we will need some folders to contain our scripts, data and results:

  • Click the New Folder icon
  • Create a folder called data and click ok
  • Following the same process, create a scripts folder and a results folder