Hands-on - Import a workflow invocation from Galaxy

• 20 min
• Easy

LabID supports importing workflow "invocations" (or "run") from a Galaxy instance (public or institutional instance).
The import currently creates a workflow run in LabID with a link to the workflow invocation in Galaxy. Input datasets that can be traced back to existing datasets in LabID will be automatically associated, however output datasets are not automatically registered currently.
Below are the steps to import a workflow that was executed in Galaxy.

Step 1 : Setup your LabID account to use Galaxy

First make sure that you have associated your Galaxy account to your LabID user.
See Setup Galaxy.

Step 2 : Workflow invocations in Galaxy

• go to your Galaxy instance and navigate to the Workflow Invocations page via the navigation menu on the left
• click on the button Open Invocations List to see the full list of passed worklfow invocations
• expand the invocation you would like to import in LabID, using the arrow on the left of the workflow invocation

Navigating to the list of workflow invocations

List of passed workflow invocations

Step 3 : Copy the invocation ID

From the expanded workflow invocation, copy the invocation id (highlighted in the screencapture below).

A workflow invocation - the id required by LabID for the import is highlighted

Step 4 : Back in LabID

• Back in LabID, navigate to the list of Workflow runs via the menu on the left.
• At the top left, click the dropdown button + New workflow run then select Import Galaxy workflow invocation.

Importing Galaxy invocation in LabID

In the following import page,

• select the Galaxy Instance from which you want to import
• paste the id of the invocation copied at the previous step
• Click Import

You can also paste the full URL to the workflow invocation in Galaxy, which is the page shown when clicking on the title of a specific workflow invocation.

You can either directly paste the invocation id (as above) or the full URL to the workflow invocation.

Resulting workflow run

Below is the newly created Workflow Run entry corresponding to the workflow invocation.
Note the special Galaxy annotation, which retains the link to the workflow invocation in the Galaxy instance.

The resulting Workflow Run in LabID

A Workflow Version is automatically created on first import !

If it's the first time a workflow invocation using this galaxy workflow is imported, an associated Workflow Version (and parent Workflow) are created in LabID upon the import of the galaxy invocation.