Getting Started with Galaxy

Dockstore supports Galaxy workflows and the Launch with Galaxy tutorial elaborates different ways to launch a Galaxy workflow. Please note that Galaxy workflows cannot be launched by the Dockstore CLI.

Galaxy instances are offered by many institutions, free and otherwise. Each come with their own advantages and users can make a choice based on their own needs.

Using Galaxy Servers

Institutions across the world maintain Galaxy instances that are often shared with the greater community for free, subsidized by grants, such as the Use Galaxy Org. These are great ways to learn and use Galaxy, and many offer valuable learning resources such as the Galaxy Training Network.

Custom Galaxy in the Cloud with Terra, AnVIL, and BioData Catalyst

Galaxy is now integrated into the Terra cloud workspace. This provides Galaxy users the ability to readily create a custom environment that they can scale to their needs. Additionally, the Terra workspace is able to access a rich data corpus hosted in the cloud, including many controlled-access datasets, thus allowing users to securely conduct analyses with this data.

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.

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.