Tutorial Feature: Easier launching of WorkflowHub & Dockstore Workflows

Author(s) orcid logoHelena Rasche avatar Helena Rasche
feature update gtn tutorials

Posted on: 12 December 2023 purlPURL: https://gxy.io/GTN:N00064

While most GTN tutorials include their associated workflow directly in the GTN, some may wish to write a tutorial about running workflows from WorkflowHub, e.g. leveraging the IWC workflow collection.

We’ve added two snippets which make that easier than ever:

Hands-on: Importing and Launching a WorkflowHub.eu Workflow
Launch gromacs-mmgbsa/main (View on WorkflowHub)

WorkflowHub is a workflow management system which allows workflows to be FAIR (Findable, Accessible, Interoperable, and Reusable), citable, have managed metadata profiles, and be openly available for review and analytics.

  1. Ensure that you are logged in to your Galaxy account.
  2. Click on the Workflow menu, located in the top bar.
  3. Click on the Import button, located in the right corner.
  4. In the section “Import a Workflow from Configured GA4GH Tool Registry Servers (e.g. Dockstore)”, click on Search form.
  5. In the TRS Server: workflowhub.eu menu you should type name:"gromacs-mmgbsa/main" galaxy TRS workflow search field, name:vgp is entered in the search bar, and five different workflows all labelled VGP are listed
  6. Click on the desired workflow, and finally select the latest available version.

After that, the imported workflows will appear in the main workflow menu. In order to run the workflow, just need to click in the workflow-run Run workflow icon.

Below is a short video showing this uncomplicated procedure:

Video: Importing from WorkflowHub

And one for Dockstore:

Hands-on: Importing and Launching a Dockstore workflow
Launch My Cool Workflow (View on Dockstore)

Dockstore is a free and open source platform for sharing reusable and scalable analytical tools and workflows.

  1. Ensure that you are logged in to your Galaxy account.
  2. Go to DockStore
  3. Click on “Galaxy” dropdown within the “Launch with” panel located in the upper right corner.
  4. Select a galaxy instance you want to launch this workflow with.
  5. You will be redirected to Galaxy and presented with a list of workflow versions.
  6. Click the version you want (usually the latest labelled as “main”)
  7. You are done!

The following short video walks you through this uncomplicated procedure:

Video: Importing from Dockstore

And one for workflows hosted natively in the GTN:

Hands-on: Importing and launching a GTN workflow
Launch Galaxy Workflow Data QC (View on GitHub, Download workflow) workflow.
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on galaxy-upload Import at the top-right of the screen
  • Paste the following URL into the box labelled “Archived Workflow URL”: https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.ga
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

You can read more about these snippets and how to use them yourself in your tutorials in the GTN Contribution Guide section on Workflows.

Funding

These individuals or organisations provided funding support for the development of this resource


Recent News

See all news

Phylogenetics tutorial takes researchers back to basics!

13 June 2024   Phylogenetics Tutorial GTN Australian BioCommons

A new Galaxy Training Network tutorial has been created to take researchers back to basics to uncover the principles of phylogenetics and how tree-building methods work. A longstanding collaboration between Professor Michael Charleston from the University of Tasmania and Australian BioCommons has delivered this self-guided tutorial featuring videos and hands-on exercises. To maximise its impact, the resource was tailored specifically to be shared globally via the Galaxy Training Network, and will form the basis of an upcoming live training workshop.

From GTN Intern to Tutorial Author to Bioinformatician

13 June 2024   single-cell training education trajectory user contributor

With growing access and interest in sequencing data, Galaxy is a knight in shining armor for wet lab scientists hoping to analyze their own data. With long term intentions of increasing access to bioinformatic analyses, the Galaxy Training Network (GTN) creates a safe space where non-computer-scientists may analyze their own data and even learn to code: an invaluable skill in today’s scientific world. Galaxy introduced me to brand new skills as an undergraduate and ultimately changed the trajectory of my career. Here is my story as a biology undergraduate with no coding experience turned GTN contributor &, eventually, coding bioinformatician: thanks to Galaxy.