Tool development for a nice & shiny subdomain
purlPURL: https://gxy.io/GTN:P00025Comment: What is a Learning Pathway?
We recommend you follow the tutorials in the order presented on this page. They have been selected to fit together and build up your knowledge step by step. If a lesson has both slides and a tutorial, we recommend you start with the slides, then proceed with the tutorial.
Discover Galaxy’s communities and learn how to create your subdomain and enrich it by writing, testing and submiting your tools on Galaxy. This learning pathway will guide you through all the steps required to build a tool for Galaxy with Planemo for batch tools and how write an interactive tool.
This learning path covers topics on how to build your subdomain, to enrich it, and create a dynamic community.
Day 1: Set up your subdomain for your community
This first part explains how to discover the already existing communities (to avoid replication), how to build your subdomain, and finally how to set up your community
Time estimation: 1 hour 45 minutes
Learning Objectives
- Define 'Special Interest Group'
- Explain the purpose of Special Interest Groups
- Learn how Special Interest Groups interact with the Galaxy governance
- Discover Galaxy's communities
- Learn how to set up a subdomain for you community
- Learn how to customize you tool panel
- Improve the looks and feel of your subdomain main page
- Determine whether you need a Galaxy Special Interest Group
- Create a Special Interest Group
- Be aware of resources for expanding your Special Interest Group
| Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|
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What's a Special Interest Group?
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| Create a subdomain for your community on UseGalaxy.eu | |||
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Creating a Special Interest Group
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Day 2: Build a batch tool
This module covers getting your package on Conda, a local Galaxy instance with Planemo, write a Galaxy tool, publish it, and make it visible on a Galaxy server.
Time estimation: 4 hours 30 minutes
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
- Learn to manage the tool panel of a subdomain for both batch and interactive tools
- Create a community reviewed table for Galaxy tools within a specific scientific domain
- Embed an interactive table in a community page
| Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|
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Creating Galaxy tools from Conda Through Deployment
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| Make your tools available on your subdomain | |||
| Creation of an interactive Galaxy tools table for your community |
Day 3: Build an interactive tool
Here we go through how to build a docker image and write the correct wrapper for your interactive tool, and then again make it visible on a Galaxy server.
Time estimation: 3 hours 30 minutes
Learning Objectives
- Discover what Galaxy Interactive Tools (GxIT) are
- Understand how GxITs are structured
- Understand how GxITs work
- Be able to dockerise a basic web application
- Be able to wrap a dockerised application as a GxIT
- Be able to test and debug a new GxIT locally and on a Galaxy server
- Be able to distribute a new GxIT for others to use
- Learn to manage the tool panel of a subdomain for both batch and interactive tools
| Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|
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Galaxy Interactive Tools
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| Make your tools available on your subdomain |
Editorial Board
This material is reviewed by our Editorial Board:
Marie Josse