Importing Galaxy Workflows into RefineryΒΆ

Before you can import Workflows from a Galaxy installation into Refinery, the following requirements have to be met:

  • You have to add a Galaxy Instance for the Galaxy installation in question to Refinery through the admin UI.

  • You have to create a Workflow Engine for this Galaxy Instance using the create_workflowengine command, which requires a Galaxy Instance id and the name of a group that should own the workflow engine, e.g. “Public”.

    >>> python create_workflowengine <instance_id> "<group_name>"

    Alternatively, you can also create a workflow engine through the admin UI, in that case, however, you have to manually assign ownership to the managers of the group that should own the workflow engine.

  • You have to annotate all workflows in the Galaxy installation that you want to import.

Once these requirements have been met, run the import_workflows command:

>>> python import_workflows

This command will attempt to import Workflows from all Workflow Engines registered in your Refinery server. All Galaxy workflows that are annotated as Refinery Workflows will be parsed and imported if annotated correctly. Annotation errors will be reported, as well as the total number of Workflows imported from each Workflow Engine.

Existing Workflows in your Refinery server will be deactivated but not deleted. Deactivated workflows can no longer be executed but their information can be accessed through the Analyses in which they were run.

Related Topics

This Page