Getting Started with Galaxy

Galaxy workflow support in Dockstore is new and a preview of more full featured support to come.

Unlike WDL and CWL, Galaxy workflows in the near term are primarily created and modified from the Galaxy workflow editor (GUI), instead of a text editor.

Additionally Galaxy workflows cannot be launched by the Dockstore CLI, or launched via a ‘Launch with’ button on the workflow information page.

Tutorial Goals

  • Learn about Galaxy
  • Create and run a basic Galaxy workflow
  • Export the workflow to a file
  • Setup a GitHub account and repository
  • Push the workflow to GitHub
  • Make a GitHub release

Create a basic Galaxy workflow

Create and run your workflow in Galaxy. Here is a tutorial for Creating, Editing, Importing Galaxy Workflows

Export the workflow to a file

In Galaxy:

  • Click on the Galaxy UI Workflow link at the top of the page.
  • Click on the workflow name to expose the drop down menu.
  • Click Download

The exported JSON file with a ‘.ga’ suffix describes the inputs, outputs, and Galaxy Tool Shed dependencies for your workflow.

Download

Download

Setting up GitHub

You will need to add the Galaxy workflow file you downloaded to a source code repository that Dockstore knows about. GitHub is a good choice, and if you are not familiar with GitHub you can use this tutorial to set up an account and repository.

Upload the workflow to GitHub

  • Go to your repository and click on the Upload Files menu item under Add Files
  • Click on the ‘choose your files’ link
  • Select your ‘.ga’ Galaxy workflow file
  • Click on ‘Commit changes’

These steps are outlined here.

Releasing on GitHub

Now that we’ve successfully created our workflow in Galaxy and tested it the workflow is ready to share with others. Making a release on GitHub will tag your GitHub repository with a version tag so you can always get back to this particular release. Follow the steps outlined here to create a release.

Next Steps

Now that you have a git repository that includes a Galaxy workflow, and you have tested it and are satisfied that it works the next step is to register it on Dockstore.

If you haven’t set up a Dockstore account follow the next tutorial to create an account on Dockstore and link third party services, which includes GitHub. Otherwise follow the instructions for workflow registration.