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

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:"mRNA-Seq BY-COVID Pipeline: Counts"

      

   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:

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

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:"mRNA-Seq BY-COVID Pipeline: Analysis"

      

   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 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)