Import a Dockstore app

This page will explain how you can use BioData Catalyst powered by Seven Bridges to import an app that is available on Dockstore. Dockstore is an open platform for sharing Docker-based apps described with the Common Workflow Language (CWL), Workflow Description Language (WDL) or Nextflow, which enables bioinformaticians to share analytical tools that can be executed in a compliant execution environment, such as BioData Catalyst powered by Seven Bridges.

BioData Catalyst powered by Seven Bridges is integrated with Dockstore, which means that you can import an app from Dockstore with a single click of a button. This process consists of two stages:

  • Navigating through Dockstore and selecting an app to launch on the Platform.
  • Completing the import process on the Platform and running the app.

As the Platform supports the Common Workflow Language, the NHLBI BioData Catalyst button is visible only for CWL apps on Dockstore. Also, please note that Dockstore is an external service and apps that are available on Dockstore are third-party apps. Therefore, the performance of such apps is not guaranteed on the Platform.

Finding an app on Dockstore

This step takes place on Dockstore.

  1. Navigate to dockstore.org in your web browser.
  2. In the top navigation bar click Search. The search screen opens.
  3. In the Search box on the left, enter the desired keyword(s).
  1. If necessary, use additional filtering options below the Search box to narrow down the search results.
  2. In the search results list, click the name of the desired app. App details page opens.
  3. (Optional) In the Recent Versions box on the right, select a different version of the app. Latest app version is selected by default.
  4. In the Launch with box click NHLBI BioData Catalyst. This takes you to the Platform.

Completing the import on the Platform

This step takes place on the Platform.

After selecting Launch with > NHLBI BioData Catalyst on Dockstore, you are taken to the Platform and presented with the app import screen.

  1. Select the project in which you want to run the app.
  2. (Optional) Change the app URL. This is the unique URL that identifies the app on the Platform and usually does not need to be changed unless there is already an app with the same URL in the project.
  3. Click Import the app. This takes you to the app details page inside the selected project.

If you want to make further edits to the app before running it, click Edit in the top-right corner. Otherwise, click Run to create a draft task, set task inputs and run the app on BioData Catalyst powered by Seven Bridges.

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Import a Dockstore app


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