Tutorial Feature: Easier launching of WorkflowHub & Dockstore Workflows

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 (v4) (View on WorkflowHub)

Launch gromacs-mmgbsa/main (v4) (View on WorkflowHub)

Tip: If this does not work

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. On the new page, select the GA4GH servers tab, and configure the GA4GH Tool Registry Server (TRS) Workflow Search interface as follows:
   1. “TRS Server”: workflowhub.eu

   2. “search query”: name:"gromacs-mmgbsa/main"

      

   3. Expand the correct workflow by clicking on it
   4. Select the version you would like to galaxy-upload import

The workflow will be imported to your list of workflows. Note that it will also carry a little blue-white shield icon next to its name, which indicates that this is an original workflow version imported from a TRS server. If you ever modify the workflow with Galaxy’s workflow editor, it will lose this indicator.

Below is a short video showing the entire uncomplicated procedure:

And one for Dockstore:

Hands On: Importing and Launching a Dockstore Workflow

Launch K-mer Profiling HiFi (v0.1.5) (View on Dockstore)

Launch K-mer Profiling HiFi (v0.1.5) (View on Dockstore)

Tip: If this does not work

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:

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 to Launch Galaxy Workflow Data QC (View on GitHub, Download workflow)

Tip: If this does not work

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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
4. Click the Import workflow button

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

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 organisations or grants provided funding support for the development of this resource

BeYond-COVID

BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response. This project has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement № 101046203 (BY-COVID)