Galaxy workflows in Dockstore

Contributors

Authors: Avani Khadilkar Elizabeth Sheets Charles Overbeck Enis Afgan

Objectives

• What is Dockstore?

• Why use Dockstore?

• How to find workflows on Dockstore?

• How to launch workflows from Dockstore?

• Getting started with Galaxy workflows on Dockstore

• Register your Galaxy workflow on Dockstore

What is Dockstore?

Dockstore: “an app store for bioinformatics”

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• Open-source platform for sharing reusable bioinformatics workflows

• Easy and reliable way to find and use relevant workflows as well as publish your own workflows

• Dockstore integrates source control repositories like GitHub, Bitbucket, and GitLab for version control and automatic updates.

• Integration with several cloud environments such as the usegalaxy.org, Galaxy Project’s public server provides a succinct infrastructure to host high quality workflows

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dockstore.org

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What is Dockstore?

Why use Dockstore?

Dockstore follows the FAIR Guiding Principles (Findable, Accessible, Interoperable and Reusable).

Findable

• Dockstore parses provided metadata and allows it to be searchable.

• With the faceted search feature, user can find workflows using search terms and filter using workflow language, author, organization, labels, etc.

• Institutions and organizations can showcase their work by research theme in the Organizations and Collections page. For example, IWCG

Why use Dockstore?

Dockstore follows the FAIR Guiding Principles (Findable, Accessible, Interoperable and Reusable).

Accessible

• Dockstore never requires a user to log in to search and inspect contents for workflows and tools.

• Once found, analyses can be launched in different environments using the Launch with feature of Dockstore. Workflows can just as easily be downloaded to run on local machines.

• Users can also request a DOI via Zenodo for their workflows for reference in published research.

Why use Dockstore?

Dockstore follows the FAIR Guiding Principles (Findable, Accessible, Interoperable and Reusable).

Interoperable

• Users are strongly encouraged to provide clear instructions, test data and checker workflows to ensure that their workflows are usable in any environment.

• The GA4GH TRS API enable the simple launching of workflows to a variety of compute platforms.

Why use Dockstore?

Dockstore follows the FAIR Guiding Principles (Findable, Accessible, Interoperable and Reusable).

Reusable

• Contributors are encouraged to provide clear documentation and the exact version of the components in their descriptor files so that others can find, reuse and build upon the workflows.

• The Dockstore GitHub App provides support for registering workflows, version control/tagging and automatically syncing workflows and services.

How to find workflows on Dockstore?

How to find workflows on Dockstore?

You can find relevant workflows using the Faceted Search option:

Scan the code below or simply click on the link to be directed to the detailed documentation.

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Faceted Search

How to find workflows on Dockstore?

You can also find workflows through the Organizations/Collections feature:

Scan the code below or simply click on the link to be directed to the detailed documentation.

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Organizations and Collections

How to launch workflows from Dockstore?

You can use the Launch With feature to launch the workflow in your choice of environment:

Scan the code below or simply click on the link to be directed to the detailed documentation.

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Launch with Galaxy

How to launch workflows from within Galaxy?

You can use the GA4GH Tool Registry Server (TRS) Workflow Search using keywords in the description of the workflows on Dockstore. Alternatively, you can use the GA4GH Tool Registry Server (TRS) Workflow Import using the TRS ID from workflow description on Dockstore.

Getting started with Galaxy workflows on Dockstore?

Get started on writing and publishing Galaxy workflows, refer to the Getting Started with Galaxy doc.

Scan the code below or simply click on the link to be directed to the detailed documentation.

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Get Started with Galaxy

Register your Galaxy workflow on Dockstore

If you have a workflow you want to register, you can follow the Getting Started with Workflows doc.

Scan the code below or simply click on the link to be directed to the detailed documentation.

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Register your workflow on Dockstore

You can also watch the “How to launch Galaxy workflows from Dockstore” videos linked below:

How to launch Galaxy workflows from Dockstore - Part 1 (Using the default cloud environment options)

How to launch Galaxy workflows from Dockstore - Part 2 (Using custom cloud environment options)

Thank you!