Galaxy workflows in Dockstore

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# Galaxy workflows in Dockstore

<div class="contributors-line">
		
	
<ul class="text-list">
			
			<li>
				<a href="/training-material/hall-of-fame/avani-k/" class="contributor-badge contributor-avani-k"><img src="https://avatars.githubusercontent.com/avani-k?s=36" alt="Avani Khadilkar avatar" width="36" class="avatar" />
    Avani Khadilkar</a>
			<li>
				<a href="/training-material/hall-of-fame/bethsheets/" class="contributor-badge contributor-bethsheets"><img src="https://avatars.githubusercontent.com/bethsheets?s=36" alt="Elizabeth Sheets avatar" width="36" class="avatar" />
    Elizabeth Sheets</a>
			<li>
				<a href="/training-material/hall-of-fame/coverbeck/" class="contributor-badge contributor-coverbeck"><img src="https://avatars.githubusercontent.com/coverbeck?s=36" alt="Charles Overbeck avatar" width="36" class="avatar" />
    Charles Overbeck</a>
			<li>
				<a href="/training-material/hall-of-fame/afgane/" class="contributor-badge contributor-afgane"><img src="https://avatars.githubusercontent.com/afgane?s=36" alt="Enis Afgan avatar" width="36" class="avatar" />
    Enis Afgan</a></li>
</ul>

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## Requirements

Before diving into this slide deck, we recommend you to have a look at:

- [Introduction to Galaxy Analyses](/training-material/topics/introduction)
    - Galaxy Basics for genomics: [<i class="fas fa-laptop" aria-hidden="true"></i><span class="visually-hidden">tutorial</span> hands-on](/training-material/topics/introduction/tutorials/galaxy-intro-101/tutorial.html)

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### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> 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

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# What is Dockstore?

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## Dockstore: “an app store for bioinformatics”

.pull-left[

- 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

]

.pull-right[

.image-60[
  ![Structure of Dockstore](/training-material/topics/galaxy-interface/images/Dockstore-Schematic.png)
]

[dockstore.org](https://dockstore.org/)

]

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# What is Dockstore?

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## 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](https://dockstore.org/organizations/iwc)

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## 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.

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## 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.

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## 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.

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# How to find workflows on [Dockstore](https://dockstore.org/)?

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## How to find workflows on [Dockstore](https://dockstore.org/)?

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.

.pull-left[.image-30[
  ![Faceted Search QR](/training-material/topics/galaxy-interface/images/FacetedSearchQR.png)]]

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![Faceted Search Screenshot](/training-material/topics/galaxy-interface/images/FacetedSearchScreenshot.png)]

[Faceted Search](https://docs.dockstore.org/en/stable/end-user-topics/faceted-search.html)

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## How to find workflows on [Dockstore](https://dockstore.org/)?

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.

.pull-left[.image-30[
  ![Organizations/Collections QR](/training-material/topics/galaxy-interface/images/OrgCollectnQR.png)]]

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![Organizations/Collections Screenshot](/training-material/topics/galaxy-interface/images/OrgCollectnScreenshot.png)]

[Organizations and Collections](https://docs.dockstore.org/en/stable/advanced-topics/organizations-and-collections.html)

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## How to launch workflows from [Dockstore](https://dockstore.org/)?

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.

.pull-left[.image-30[
  ![Launch With QR](/training-material/topics/galaxy-interface/images/LaunchWithQR.png)]]

.pull-right[
![Launch With Screenshot](/training-material/topics/galaxy-interface/images/LaunchWithScreenshot.png)]

[Launch with Galaxy](https://docs.dockstore.org/en/stable/launch-with/galaxy-launch-with.html)

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## How to launch workflows from within [Galaxy](https://usegalaxy.org/)?

You can use the [GA4GH Tool Registry Server (TRS) Workflow Search](https://usegalaxy.org/workflows/trs_search) using keywords in the description of the workflows on Dockstore.
Alternatively, you can use the [GA4GH Tool Registry Server (TRS) Workflow Import](https://usegalaxy.org/workflows/trs_import) using the TRS ID from workflow description on Dockstore.

![Launch From Galaxy Search](/training-material/topics/galaxy-interface/images/LaunchGalaxySearch.png)
![Launch From Galaxy TRS ID](/training-material/topics/galaxy-interface/images/LaunchGalaxyTRSID.png)

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## Getting started with Galaxy workflows on [Dockstore](https://dockstore.org/)?

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.

.pull-left[.image-40[
  ![Getting Started QR](/training-material/topics/galaxy-interface/images/GettingStartedQR.png)]]

.pull-right[
![Getting Started Screenshot](/training-material/topics/galaxy-interface/images/GettingStartedScreenshot.png)]

[Get Started with Galaxy](https://docs.dockstore.org/en/stable/getting-started/getting-started-with-galaxy.html)
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## Register your Galaxy workflow on [Dockstore](https://dockstore.org/)

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.

.pull-left[.image-40[
![Getting Started with Workflows QR](/training-material/topics/galaxy-interface/images/GettingStartedWorkflowsQR.png)]]

.pull-right[
![Getting Started with Workflows Screenshot](/training-material/topics/galaxy-interface/images/GettingStartedWorkflowsScreenshot.png)]

[Register your workflow on Dockstore](https://docs.dockstore.org/en/stable/getting-started/dockstore-workflows.html)

---

## 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)](https://youtu.be/U8rQiwLceZg)

[How to launch Galaxy workflows from Dockstore - Part 2 (Using custom cloud environment options)](https://youtu.be/aYShFs9tZ6s)

---

## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

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<table class="contributions">
	
	<tr>
		<td><abbr title="These people wrote the bulk of the tutorial, they may have done the analysis, built the workflow, and wrote the text themselves.">Author(s)</abbr></td>
		<td>
			<a href="/training-material/hall-of-fame/avani-k/" class="contributor-badge contributor-avani-k"><img src="https://avatars.githubusercontent.com/avani-k?s=36" alt="Avani Khadilkar avatar" width="36" class="avatar" />
    Avani Khadilkar</a><a href="/training-material/hall-of-fame/bethsheets/" class="contributor-badge contributor-bethsheets"><img src="https://avatars.githubusercontent.com/bethsheets?s=36" alt="Elizabeth Sheets avatar" width="36" class="avatar" />
    Elizabeth Sheets</a><a href="/training-material/hall-of-fame/coverbeck/" class="contributor-badge contributor-coverbeck"><img src="https://avatars.githubusercontent.com/coverbeck?s=36" alt="Charles Overbeck avatar" width="36" class="avatar" />
    Charles Overbeck</a><a href="/training-material/hall-of-fame/afgane/" class="contributor-badge contributor-afgane"><img src="https://avatars.githubusercontent.com/afgane?s=36" alt="Enis Afgan avatar" width="36" class="avatar" />
    Enis Afgan</a>
		</td>
	</tr>

<tr class="reviewers">
		<td><abbr title="These people reviewed this material for accuracy and correctness">Reviewers</abbr></td>
		<td>
			<a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-badge-small contributor-hexylena"><img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/avani-k/" class="contributor-badge contributor-badge-small contributor-avani-k"><img src="https://avatars.githubusercontent.com/avani-k?s=36" alt="Avani Khadilkar avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-badge-small contributor-bgruening"><img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/shiltemann/" class="contributor-badge contributor-badge-small contributor-shiltemann"><img src="https://avatars.githubusercontent.com/shiltemann?s=36" alt="Saskia Hiltemann avatar" width="36" class="avatar" /></a></td>
	</tr>

</table>

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Tutorial Content is licensed under <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.<br/>