Using workflows from a private GitHub

Allie Cliffe
  • Updated

Step-by-step instructions to import workflows from a private GitHub to run in Terra on Azure (Enterprise customers).

Step 1: Set up credentials in GitHub (one time only)

1.1. Navigate to the Profile page from the main menu (three lines at the top left > {your name} > Profile). 


1.2. Select the External Identities tab. 


1.3. Click the blue "Link to your GitHub account" button. 


What to expect/next steps

You'll be redirected to Github to authorize your account. Once the terms are accepted, you’ll be redirected back to Terra to import a workflow from your linked GitHub (after installing the GitHub app - step below).

Step 2: Install GitHub app locally

2.1. Navigate to

2.2. Select the green Install button (right side).

Screenshot of Terra App on GitHub

2.3. Select the organization or user you want to install the app into from the dropdown.
If you're testing this new feature, your repositories may be on your personal account and not attached to an organization, just select your username from the list.


2.4. Select which repositories the app should have access to.

You can choose to install the app on all repositories (screenshot at left below) or on select ones (right screenshot below), such as any repositories marked as private.

Screenhot-of-repositories-the-GitHub-app-should-have-access-to-with-radio-button-for-all-repositories-selected.png Screenshot-of-Authorize-and-request-screen-with-only-select-respositories-radio-button-selected-and-a-blank-search-field.png

2.5. Install and authorize. 

Step 3: Import workflow

3.1. In the workspace Workflows tab, click on Find & add workflows in the left-hand panel.

Screenshot showing the Workflows tab of an example workspace. An orange rectangle highlights the 'Find & add workflows' option on the left-hand panel.

3.2. Select Import a workflow.

3.3. Fill in the GitHub link and workflow name in the blank fields and click the Add to Workspace button (the button will be disabled if every field is not filled in).

Screenshot showing the menu used to add a workflow directly from GitHub to an example workspace. Orange rectangles highlight the 'Import a Workflow' button on the left-hand panel and the 'Github link' and 'workflow name' fields used to import the workflow.

How to find the workflow link

You can access the correct GitHub link in three ways: from Terra, from Dockstore, and directly from GitHub.

  • 3.4. If you've already imported an earlier version of the workflow into your Terra workspace, open the workflow from the workspace's Workflows tab. 

    3.5. Click on the Source link in the workflow's configuration menu. This will surface the source link for the workflow.

    Screenshot of the workflow configuration page for an example workflow on Terra. An orange rectangle highlights the Source link, which is just below the Version drop-down menu.

  • 3.4. Go directly to

    3.5. Log in and click on My Dockstore.

    Screenshot of the Dockstore homepage. An orange rectangle highlights the My Dockstore button with a speedometer icon at the top right of the page.

    3.6. Select Workflows from the left-hand panel of the My Dockstore dashboard.

    3.7. Choose your workflow.

    3.8. Click on the workflow's Info tab and then click on the Source code link under the Workflow Information section to find the GitHub source link.

    Screenshot showing an example My Dockstore screen on the Dockstore website. Orange rectangles highlight (1) the Workflows button on the left-hand panel, (2) an individual workflow, and (3) the Source Code link for that workflow. Click (1) and (2) in order to see (3).

  • 3.4. Go directly to

    3.5. Log in and navigate to your repositories.

    3.6. Select the repository used for the workflow.

    3.7. Right-click on your workflow's file and select copy link.


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