AnVIL Guides and FAQ

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Last updated: November 2025

Guides

FAQs

Access the class workspace

Each class that uses AnVIL will have its own workspace. Your instructor will need to add you to the workspace through your email before you can access it.

  1. Open AnVIL in Google Chrome
  2. Click on the hamburger icon in the top left corner
  3. Sign in to your AnVIL account
  4. Click on the hamburger icon in the top left corner again
  5. Click workspaces
  6. Click on the workspace name to enter the workspace.

Create an RStudio Environment

When you open the workspace, you will be on the dashboard tab by default. The dashboard contains the instructions on how to use the workspace, links to C-MOOR websites, and the startup script.

  1. Take note of the container image for the custom environment. We recommend copying this to a word document or notepad. Make sure there are no spaces before or after what you copy. You will need to input this URL soon.
  2. Take note of the startup script. We recommend copying this to a word document or notepad. Make sure there are no spaces before or after what you copy. You will need to input this URL soon.
  3. Click on the Environment Configuration button (cloud with lightning).
  4. In the RStudio section, click Settings.
  5. Make sure you have the following settings matching these instructions. Under Application configuration, choose “Custom environment”. In the container image field that appears, paste the container image URL that we copied earlier from the workspace. The URL should end with Bioconductor 3.19.1. In the startup script field, paste the URL for the startup script. This URL contains the words C-MOOR Startup Script. Set the creation timeout limit to 15 minutes.
  6. Select 4 CPUs and 15 gigabytes of memory.
  7. Confirm that the cloud compute cost is 20 cents per hour. If it is not 20 cents per hour, reselect CPUs and memory allocation in step 6. This is a known bug in AnVIL at the time of writing of this guide.
  8. Scroll to the bottom of the window and click “Create”. It will take some time for the RStudio Environment to be created. You can keep track of the status of the environment based on the colored dot next to the RStudio icon. The dot will turn green when the environment is ready. While it is loading (blue), you cannot interact with it.
  9. When the environment is ready, use the Open RStudio button that will pop up. You can also access RStudio through the Analyses tab. If you hold down Ctrl as you click, you can open RStudio in a new window.

Launch a module

  1. Use the file explorer in RStudio to navigate to your module of choice. Enter the folder of the curriculum your class is using, then enter the module’s folder.
  2. In the module’s folder, open the .Rmd file by double clicking its name.
  3. Click Run Document in the top left area in the open .Rmd file to run it. Note that the Run Document button is different from the Run button!

Close out a session on AnVIL

You should be deleting your RStudio environment every time you run a module. Do not leave it running overnight as you will continue to run up charges on your class workspace (note that this is paid by your instructor or university)!

  1. On the right side of the screen, click the Cloud Environment button. This is the cloud with the lightning symbol.
  2. Under the RStudio section, click settings.
  3. Scroll to the bottom of the new window and click delete environment.
  4. Check Delete everything, including the persistent disk or your instructor’s billing account will incur costs for storage.

FAQ

I don’t see my class workspace

Confirm with your instructor that they added you to the workspace. For them to do so, you need to have shared the email you used to sign up for AnVIL with them. As a reminder, this needs to be a Google associated email (uses Gmail) to be able to use the Google cloud resources the modules need.

I see “Google is syncing permissions” and can’t continue

This could be a number of different things. If refreshing the page doesn’t work, confirm with your instructor that their billing account is still active. If it is, confirm there are no disruptions to Google Cloud and/or try another time. If another student has a working workspace, buddy up with them for the time being.

The file explorer is empty

This means that you forgot to add the startup script when you were creating the RStudio container. Delete the container and make a new one with the correct settings.

My code times out or takes too long

This means you didn’t include the correct version of Bioconductor, likely by forgetting to include the custom environment field when you were creating the RStudio container. Delete the container and make a new one with the correct settings.

Alternatively, it may mean your environment doesn’t have enough computational power. Delete the container and make a new one with the correct settings (4CPUs).