Learn to use MINERVA Platform's COVID-19 Disease Map with Galaxy

by-covid pathways minerva gtn infrastructure new feature

Posted on: 28 March 2024 purlPURL: https://gxy.io/GTN:N00076

As part of the work of BeYond COVID, we have developed a new integration between the MINERVA Platform’s COVID-19 Disease Map and Galaxy! Datasets created within Galaxy can now be seamlessly visualized in the MINERVA Platform, allowing you to explore your data in the context of the COVID-19 Disease Map.

This work generated a number of brand new WorkflowHub Workflows, which can now be launched more easily than ever in the GTN:

Hands-on: Importing and Launching a WorkflowHub.eu Workflow
Launch mRNA-Seq BY-COVID Pipeline: Counts (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:"mRNA-Seq BY-COVID Pipeline: Counts" 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

Hands-on: Importing and Launching a WorkflowHub.eu Workflow
Launch mRNA-Seq BY-COVID Pipeline: Analysis (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:"mRNA-Seq BY-COVID Pipeline: Analysis" 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 a few new GTN features like the ability to embed a workflow visualisation directly into a tutorial. Go check it out!

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Funding

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


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