Module: Galaxy Development

The Galaxy for Developers module will teach you how Galaxy works internally (frontend and backend), how to add new features for Galaxy, how to build the best tools and visualisations, and more!

Galaxy Development

Ever wanted to contribute features to Galaxy? Here you’ll learn a bit about how Galaxy works and how to debug issues in features in Galaxy.

This series of videos will guide (future) Galaxy contributors through the process of debugging Galaxy.

Introduction (Tutorial)

Description:

This is the first video in the Debugging Galaxy series.
Length: 11 minutes
Captions: Dave Clements
Created: 15 February 2021
Materials:
Support:
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Unit Testing (Tutorial)

Description:

What to do when a unit test fails.
Length: 14 minutes
Captions: John Davis
Created: 15 February 2021
Materials:
Support:
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API tests (Tutorial)

Description:

What to do when an API test fails.
Length: 23 minutes
Captions: John Davis
Created: 15 February 2021
Materials:
Support:
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Client Unit Tests (Tutorial)

Description:

What to do when your client throws a unit test failure.
Length: 6 minutes
Captions: Beatriz Serrano-Solano
Created: 15 February 2021
Materials:
Support:
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Client Linting (Tutorial)

Description:

This video covers working through the client linting error hit in the previous tutorial.
Length: 6 minutes
Captions: Beatriz Serrano-Solano
Created: 15 February 2021
Materials:
Support:
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Selenium (Tutorial)

Description:

Selenium is used to test Galaxy development. Learn more about test failure and how to address them.
Length: 18 minutes
Captions: Assunta DeSanto, John Davis, Dave Clements, Beatriz Serrano-Solano
Created: 15 February 2021
Materials:
Support:
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Runtime Errors (Tutorial)

Description:

How to fix a runtime error
Length: 40 minutes
Captions: John Davis
Created: 15 February 2021
Materials:
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Debugging Wisdom (Lecture)

Description:

A summary of wisdom to debug Galaxy with.
Length: 3 minutes
Captions: Dave Clements
Created: 15 February 2021
Materials:
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Tool Development

This module covers everything you need to start developing your own Galaxy Tools. This module will likely take you several days to complete.

Tutorial Video

Description:
  1. The first step to adding a tool to Galaxy, is to add it to (Bio)Conda. This tutorial will show you how to do that.
  2. Planemo is the Galaxy tool development kit, and will make your tool development process a lot easier! This tutorial will show you how to use Planemo to start the tool wrapping process, and covers the general structure of a Galaxy tool wrapper.
  3. You are now ready to start writing your tool wrapper! This video will show you how.
  4. Each tool wrapper also needs a .shed.yml file, which contains some metadata about the tool.
  5. Here you will learn how to test Galaxy tools using Planemo.
  6. Here you will learn how to publish tools in public tool repositories.
Length: 40 minutes
Captions: Cristóbal Gallardo
Created: 11 March 2022
Materials:
Support:
Learning Objectives:
  • Learn how to make and deploy a conda package
  • Understand how to write a Galaxy tool wrapper
  • Be able to use a tool wrapper locally
  • Be able to test the tool wrapper
  • Learn how to add tools to the Galaxy toolshed and make them available to any user
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Galaxy Training Material Development

Here you can learn about contributing to the GTN’s development, adding new tutorials or slides, and correcting any typos you might spot in the training materials this week.

Tutorial Video

Description:

This tutorial will show you how you can preview your contributions to the GTN online using GitPod.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Preview the GTN website online via GitPod
  • Make changes to the GTN website and preview those changes
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Tutorial Video

Description:

This tutorial will go through all of the steps of creating a simple tutorial and contributing it to the GTN.
Length: 42 minutes
Captions: Engy Nasr
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Create a tutorial from scratch
  • Link a tutorial to a topic
  • Create hands-on
  • Add technical support for a tutorial
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Lecture Video

Description:

This lecture goes through the process of how to create a slide deck, common things you should bear in mind while you’re writing them, and how to enable the amazing slides-to-video features for your slide decks! This video itself was produced automatically from the GTN’s slide decks, anyone making edits to these slides will cause them to be rebuilt, making organising videos for events easier than ever.
Length: 5 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Create a new set of slides
  • Add presenter comments
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