DNAnexus Basics

Setting up the R-Studio environment outside of Class hours

These instructions should be followed if you are setting up the R-Studio Web environment outside the normal class hours.

Log into DNAnexus

Each student should log into their account and navigate to the R_Class_June_2022 project.

To Start the Application

From within the R_Class_June_2022, click on the application "Practicing R - Outside of Class". This will take you to a window that looks like this:

On this screen click on the "Inputs" box and select "rstudio_dir.tar.gz" from the files presented (remember to click the Select button) Having selected the appropriate Input file, start the application by clicking on the Run as Analysis button in the top right. Having started the analysis, the screen will present the "Monitor" screen, where the job will first appear in the "waiting" state before switching to "Running" (this could take a few minutes).

Open the R-Studio Web interface

Once the job is running, wait about 4 minutes before clicking on the web address shown to the right of job status line. (It will look similar to this "https://job-GBb1xFQ0YKq8PqYJKx1bVv6v.dnanexus.cloud") The reason for waiting ~4 minutes is to give the system enough time to get everything in place. If you click too soon you will see the following screen.
Don't PANIC, just wait a little longer and refresh the screen, until you are finally presented with the R-Studio login screen.

Proceed with running content from the R Class

From the login screen, login with the username/passwd "rstudio/rstudio", and proceed from there.

Splitting the window - If you wish to integrate the class notes into the same window as the RStudio interface, click on one of two file options "HSplit.html" or "VSplit.html" (found in the lower right hand segment) and select the View in Browser option from the pop-up menu. This will add the class notes to either the top portion of the browser window or to the right of the browser window. The bar separating the class notes window from the R-studio interface can be dragged up and down or left to right to change the size of the window dedicated to each function.

If you encounter any problems send email to BTEP at ncibtep@nih.gov