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Connecting GitHub to Verily Workbench

Why it matters

Verily Workbench is where you run analyses; GitHub is where the CRN's pipeline code, tutorials, and notebooks actually live. Connecting a GitHub repo to a workspace is what bridges the two — it's the link between the CRN Cloud's "Resources & Documentation" pillar and its "Data Utilization: Analysis & Sharing" pillar.

Concretely, once a repo is connected to your workspace, it's automatically cloned into every app (JupyterLab, RStudio, etc.) you launch from that workspace. That means:

  • No manually downloading or uploading scripts between your laptop and the cloud
  • Your notebooks stay in sync with the latest version of the pipeline/tutorial code
  • Your analysis, the code that produced it, and its version history all live together — which is what makes the work reproducible and shareable with the rest of the team

How to connect a repo

  1. Open your workspace and go to the Apps tab.
  2. Click + Add Repository within the Git repositories section.
  3. Enter a Name for the repo (e.g., asap-crn-learning-lab).
  4. Enter the Repository URL (e.g., https://github.com/ASAP-CRN/asap-crn-learning-lab).
  5. Click Add Repository.

Once added, the repo will be cloned automatically into any app you create in that workspace going forward.

Repositories are typically available under: $HOME/repos

For example, the Learning Lab repository may appear at: $HOME/repos/asap-crn-learning-lab/

Important note about existing apps

Adding a repository to a workspace does not automatically add it to apps that were already created.

If you added the repository after creating your app, either create a new app or clone the repository manually from inside the existing app.

From a terminal inside the app, you can use: wb git clone --resource=<YOUR_GITHUB_RESOURCE_NAME> or clone directly from GitHub: git clone <REPO_URI>

  • Link the repo directly if you just want to run or lightly explore existing notebooks.
  • Fork it first, then connect your fork's URL, if you plan to modify code or contribute changes back.

For more in-depth information refer to Working with GitHub