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

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 (v1) (View on WorkflowHub)

Launch mRNA-Seq BY-COVID Pipeline: Counts (v1) (View on WorkflowHub)

Tip: If this does not work

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"
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:

Hands-on: Importing and Launching a WorkflowHub.eu Workflow

Launch mRNA-Seq BY-COVID Pipeline: Analysis (v1) (View on WorkflowHub)

Launch mRNA-Seq BY-COVID Pipeline: Analysis (v1) (View on WorkflowHub)

Tip: If this does not work

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"
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:

And a few new GTN features like the ability to embed a workflow visualisation directly into a tutorial. Go check it out!

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)