GCC2021 Developer Training Track

Supporting Materials

Slides: Welcome & Course Information
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Slack channel: #event-gcc2021 - Have question about the training? Did you run into a problem? Just wanna chat? Ask an Instructor on Slack!
Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: #event-gcc2021 ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet (hashtag #usegalaxy), and follow the GTN on Twitter! @gxytraining

Most of these training sessions require you to have some prior setup to begin them.

Windows

You will need WSL2 installed
Having git installed will help you for a number of the tutorials which work with Galaxy.

OSX/Linux

Having git installed will help you for a number of the tutorials which work with Galaxy.

Certificates of attendance can be requested after the training week.

Requirements

Have a registration for the GCC2021 Training Week
Keep all your Galaxy histories

We will ask you to provide links to the histories for all sessions you followed
If a tutorial does not create a Galaxy history (e.g. developer training), keep any other outputs you may create during the training session

Answer the dailiy icebreakers question on Slack every day
Be active on Slack!

Join the Slack channels for every training session you follow this week (links under "supporting materials" at the bottom of each session)
Let us know when you are starting with a session in the session's dedicated Slack channel
Talk about the session! Get stuck? Have a question about the science? want to discuss anything? do it in Slack!
Whenever you finish a session, let us know on Slack that you have completed the tutorial, and let us know what you thought of it!

NOTE: You can follow as few or as many training sessions as you want, we will give you a personalized certificate listing all the sessions you attended.

Request now!

Please fill in this this Certificate Request Form

Deadline: no later than July 11, 2021.

Note: only fill in this form when you have completed all the training session you want to.

Tutorial

Video Length: 5m
Subtitles By: Saskia Hiltemann
Description: This short video gives an overview of the worldwide Galaxy community, and different ways you can get involved! Video created by Beatriz Serrano-Solano.
Training Material: GalaxyProject Home, Galaxy servers, Galaxy Training Network, Support, Galaxy Publications, Galaxy Communities, Events, Mailing Lists, Galaxy Working Groups, GitHub, Gitter Chat, GTN Gitter, PaperCuts, GTN CoFest, Twitter, Twitter

Speaker

The Global GTN Community

Supporting Materials

GalaxyProject Home: galaxyproject.org
Galaxy servers: Find a Galaxy server near you!
Galaxy Training Network: Start learning Galaxy
Support: Galaxy Help Forum
Galaxy Publications: Zotero
Galaxy Communities: Find and Join a community
Events: Galaxy Event Horizon
Mailing Lists: Stay informed of Galaxy activity!
Galaxy Working Groups: Find and join a WG
GitHub: galaxyproject
Gitter Chat: Start talking with the Galaxy Community!
GTN Gitter: Join the training discussion here!
PaperCuts: Monthly Collaboration Fest
GTN CoFest: Everybody Welcome!
Twitter: follow @galaxyproject
Twitter: follow the GTN @gxytraining
Slack channel: - Have question about the training? Did you run into a problem? Just wanna chat?
Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: . Thanks!
Enjoyed it? - Like the video on YouTube, Tweet (hashtag #usegalaxy), and follow the GTN on Twitter! @gxytraining

Webinar Series: Galaxy Resources For..

Each of the 4 webinars in this series that ran earlier this year highlights avaialble Galaxy resources for a different audience. These videos are a nice way to get an overview of what Galaxy has to offer for different types of users.

..Researchers

Video Length: 1h10m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: Wondering how to get started, or how to do a particular type of analysis, or how to scale to thousands of datasets? This webinar will highlight how to find the resources and help you need for each of these questions and more.
Training Material: Galaxy Webinar Page

Speaker

Dave Clements

..Educators and Trainers

Video Length: 1h10m
Subtitles By: Saskia Hiltemann
Description: Galaxy is an exceptional resource for teaching bioinformatics and other data sciences. The Galaxy Platform itself makes sophisticated analysis tools and workflows accessible to learners without requiring them to become system administrators or learn command line interfaces. Galaxy is a graphical user interface that only requires a browser, and allows students and teachers to focus on concepts, rather than compute infrastructure.
Training Material: Galaxy Webinar Page

Speaker

Saskia Hiltemann

Miaomiao Zhou

Avans Hogeschool

Christine Cucinotta

Fred Hutchinson Cancer Research Center

Subina Mehta

University of Minnesota

Bérénice Batut

..Tool Developers

Video Length:
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: Galaxy is an excellent platform for increasing the visibility and use of computational tools in any domain that Galaxy has been applied to. If you develop computational analysis or visualization tools then this webinar will demonstrate how porting your tools to Galaxy can significantly increase their visibility and adoption.
Training Material: Galaxy Webinar Page

Speaker

Daniel Blankenberg

Cleveland Clinic

Anthony Bretaudeau

INRAE

Petr Novák

..Administrators & Infrastructure Providers

Video Length:
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: Galaxy can empower your community to create and run their own sophisticated and repeatable data analyses and visualizations, without requiring them to learn command line interfaces or Linux systems administration. If you are interested in helping your researchers help themselves with their data analyses, then this webinar is for you. We will cover resources available in the Galaxy ecosystem to help those who setup and maintain production Galaxy servers.
Training Material: Galaxy Webinar Page

Speaker

Gianmauro Cuccuru

Lucille Delisle

Swiss Federal Institute of Technology Lausanne

Supporting Materials

Galaxy Webinar Page: View past & upcoming webinars
Slack channel: #event-gcc2021 - Have question about the training? Did you run into a problem? Just wanna chat? Ask an Instructor on Slack!
Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: #event-gcc2021 ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet (hashtag #usegalaxy), and follow the GTN on Twitter! @gxytraining

At the beginning of each day, say hi in Slack and let us know are getting started by answering the following icebreaker questions!

Monday Icebreaker Question

Let us know where you are from, and one fun fact about yourself!

Post your answers in #social on Slack!

Tuesday Icebreaker Question

What is the coolest, most mind blowing fact (nature/people/animal etc.) you know?

Post your answers in #social on Slack!

Wednesday Icebreaker Question

What is your favorite dish (food or drink)? Bonus points for recipes!

Post your answers in #social on Slack!

Thursday Icebreaker Question

1. If you had a time machine, what is the first place & time you would visit? why?
OR
2. What is your favourite book, tv show, movie or game that you would recommend to others?

Post your answers in #social on Slack!

Friday Icebreaker Question

What has been you favourite part of this training week? And what are you looking forward to most during the rest of GCC (if you are attending)?

Post your answers in #social on Slack!

And of course please feel free to respond to anybody here, this channel is for socializing and getting to know each other :)

Note: Please do this every day if you would like to receive a certificate of attendance

Galaxy 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

Here you will creating Galaxy tools from scratch using Conda for requirements, Planemo for testing, and Git for deployment. You can find the tutorial for these videos here on the GTN

Conda

Video Length: 8m
Subtitles By: Dave Bouvier
Description: 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.
Training Material: Tutorial

Speaker

Dave Bouvier

Planemo Init & Tool Structure

Video Length: 2m
Subtitles By: Alex Ostrovsky
Description: 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.
Training Material: Tutorial

Speaker

Alex Ostrovsky

Writing the tool wrapper

Video Length: 17m
Subtitles By: Alex Ostrovsky
Description: You are now ready to start writing your tool wrapper! This video will show you how.
Training Material: Tutorial

Speaker

Alex Ostrovsky

Writing the .shed.yml file

Video Length: 1m
Subtitles By: Alex Ostrovsky
Description: Each tool wrapper also needs a .shed.yml file, which contains some metadata about the tool.
Training Material: Tutorial

Speaker

Alex Ostrovsky

Testing with Planemo

Video Length: 41m
Subtitles By: Matthias Bernt
Description: Here you will learn how to test Galaxy tools using Planemo.
Training Material: Tutorial

Speaker

Matthias Bernt

UFZ - Helmholtz Centre for Environmental Research

Contributing the tool back to a public repository

Video Length: 30m
Subtitles By: Matthias Bernt
Description: Here you will learn how to publish tools in public tool repositories.
Training Material: Tutorial

Speaker

Matthias Bernt

UFZ - Helmholtz Centre for Environmental Research

Supporting Materials

Tutorial: Galaxy Tools: From Conda Through Deployment
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Slack channel: #dev-tools-conda - Have question about the training? Did you run into a problem? Just wanna chat? Ask an Instructor on Slack!
Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: #dev-tools-conda ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet (hashtag #usegalaxy), and follow the GTN on Twitter! @gxytraining

Instructors

The following instructors are available online this week for support for this session:

Dave Bouvier

Matthias Bernt

UFZ - Helmholtz Centre for Environmental Research

Alex Ostrovsky

The Global GTN Community

Hall of Fame

Tutorial

Here you can learn about a specialised Galaxy tool that generates tool wrappers for supplied analysis scripts. Generated tools are immediately installed and ready to run, and can be edited and re-generated in Galaxy. It lacks many advanced features (e.g. filters) but is easy to learn to use for those useful scripts that do not require them. Prerequisites: Linux shell and scripting skills are required. A Linux/Docker workstation or high-end laptop is needed for Appliance installation.

There are two hands-on tutorials associated with this session:

Introductory hands-on DIY tutorial - obtaining the Appliance and creating “hello world” tools using the ToolFactory
Exploring the demonstration tools in depth and some handy ToolFactory features. There is no particular curriculum - developers will want to explore their own needs. The Appliance encourages learning by doing. It provides instant feedback when a tool is (re)generated.

Brief Overview

Video Length: 3m
Subtitles By: The Global GTN Community
Description: Making tools from command-line scripts with the ToolFactory.
Training Material: Tutorial, Tutorial

Speaker

These slides are narrated by AWS Polly.

Your first "Hello world" tools using Galaxy as an integrated development environment

Video Length: 7m
Subtitles By: Ross Lazarus
Description: Hands on demonstration for the Introductory tutorial. Create, run and update a “Hello World” tool in Galaxy
Training Material: Tutorial, Tutorial

Speaker

Ross Lazarus

Long story

Video Length: 30m
Subtitles By: Ross Lazarus
Description: ToolFactory Presentation: Abstract tool interface code that wraps simple scripts can be generated using a Galaxy tool. If you haven’t already decided that the GTN tutorials linked below might be useful for your work, or if want to hear Ross’s opinions on tools, abstract interfaces and why they matter, this talk is for you.
Training Material: Tutorial, Tutorial

Speaker

Ross Lazarus

Supporting Materials

Tutorial: ToolFactory: Generating Tools From Simple Scripts
Tutorial: ToolFactory: Generating Tools From More Complex Scripts
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Slack channel: #dev-toolfactory - Have question about the training? Did you run into a problem? Just wanna chat? Ask an Instructor on Slack!
Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: #dev-toolfactory ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet (hashtag #usegalaxy), and follow the GTN on Twitter! @gxytraining

Instructors

The following instructors are available online this week for support for this session:

Ross Lazarus

The Global GTN Community

Hall of Fame

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

Learn to contribute to the GTN! Everything from tutorials to slides, small edits and big are welcome and here you’ll learn how.

GitPod for contributing to the GTN.

Video Length: 20m
Subtitles By: Saskia Hiltemann
Description: This tutorial will show you how you can preview your contributions to the GTN online using GitPod.
Training Material: Tutorial 1, Tutorial 2, Related tutorial, Slides

Speaker

Saskia Hiltemann

Creating a new Tutorial

Video Length: 42m
Subtitles By: Engy Nasr
Description: This tutorial will go through all of the steps of creating a simple tutorial and contributing it to the GTN.
Training Material: Tutorial 1, Tutorial 2, Related tutorial, Slides

Speaker

Bérénice Batut

Creating Slides

Video Length: 5m
Subtitles By: The Global GTN Community
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.
Training Material: Tutorial 1, Tutorial 2, Related tutorial, Slides

Speaker

These slides are narrated by AWS Polly.

Supporting Materials

Tutorial 1: Running the GTN website online using GitPod
Tutorial 2: Creating a new tutorial
Related tutorial: Creating content in Markdown
Slides: Creating Slides for the GTN
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Slack channel: #contributing-gtn - Have question about the training? Did you run into a problem? Just wanna chat? Ask an Instructor on Slack!
Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: #contributing-gtn ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet (hashtag #usegalaxy), and follow the GTN on Twitter! @gxytraining

Instructors

The following instructors are available online this week for support for this session:

Saskia Hiltemann

Bérénice Batut

Helena Rasche

Avans Hogeschool

Simon Gladman

University of Melbourne

The Global GTN Community

Hall of Fame

Galaxy Core 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.

Tutorial

In this tutorial we will demonstrate how to find and fix common types of bugs you may encounter as a contributor to Galaxy. We will step you through the process of finding and fixing a bug - from locating specific errors in the logs of Galaxy’s GitHub Actions, to identifying their cause, developing a solution and committing your edits.

Intro

Video Length: 11m
Subtitles By: Dave Clements
Description: This is the first video in the Debugging Galaxy series.
Training Material: Tutorial

Speaker

Assunta DeSanto

Sergey Golitsynskiy

Fix a failing unit test

Video Length: 14m
Subtitles By: Sergey Golitsynskiy
Description: What to do when a unit test fails.
Training Material: Tutorial

Speaker

Assunta DeSanto

Sergey Golitsynskiy

API Test Failure

Video Length: 23m
Subtitles By: Sergey Golitsynskiy
Description: What to do when an API test fails.
Training Material: Tutorial

Speaker

Assunta DeSanto

Sergey Golitsynskiy

Client Unit Test Failure

Video Length: 6m
Subtitles By: Beatriz Serrano-Solano
Description: What to do when your client throws a unit test failure.
Training Material: Tutorial

Speaker

Assunta DeSanto

Sergey Golitsynskiy

Client Linter

Video Length: 6m
Subtitles By: Beatriz Serrano-Solano
Description: This video covers working through the client linting error hit in the previous tutorial.
Training Material: Tutorial

Speaker

Assunta DeSanto

Sergey Golitsynskiy

Selenium Test Failures

Video Length: 18m
Subtitles By: Assunta DeSanto, Sergey Golitsynskiy, Dave Clements, Beatriz Serrano-Solano
Description: Selenium is used to test Galaxy development. Learn more about test failure and how to address them.
Training Material: Tutorial

Speaker

Assunta DeSanto

Runtime Error

Video Length: 40m
Subtitles By: Sergey Golitsynskiy
Description: How to fix a runtime error
Training Material: Tutorial

Speaker

Sergey Golitsynskiy

Conclusion

Video Length: 3m
Subtitles By: Dave Clements
Description: A summary of wisdom to debug Galaxy with.
Training Material: Tutorial

Speaker

Assunta DeSanto

Sergey Golitsynskiy

Supporting Materials

Tutorial: Debugging Galaxy
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Slack channel: #dev-debugging-galaxy - Have question about the training? Did you run into a problem? Just wanna chat? Ask an Instructor on Slack!
Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: #dev-debugging-galaxy ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet (hashtag #usegalaxy), and follow the GTN on Twitter! @gxytraining

Instructors

The following instructors are available online this week for support for this session:

Sergey Golitsynskiy

Assunta DeSanto

John Chilton

Dannon Baker

The Global GTN Community

Hall of Fame

Galaxy Architecture Lectures

Here you’ll learn about the internals of Galaxy in a lecture from John Chilton

Lecture Series & Self-study Tutorial

This lecture series will cover:

How is the Galaxy code structured?
What do the various other projects related to Galaxy do?
What happens when I start Galaxy

As Galaxy evolves, these lectures will also be updated. The latest version of these videos can always be seen in this YouTube playlist: bit.ly/gx-arch-vids

There is also a GTN tutorial (self-study) which will walk you through contributing to the Galaxy core code base. See supporting materials at the bottom of this session to find this tutorial.

Ecosystem

Video Length: 25m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: TODO
Training Material: Slides, Self-study tutorial, Youtube Playlist

Speaker

John Chilton

Project Management

Video Length: 25m
Subtitles By: Mallory Freeberg
Description: TODO
Training Material: Slides, Self-study tutorial, Youtube Playlist

Speaker

John Chilton

Principles

Video Length: 5m
Subtitles By: Saskia Hiltemann
Description: TODO
Training Material: Slides, Self-study tutorial, Youtube Playlist

Speaker

John Chilton

Files and Directories

Video Length: 17m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: TODO
Training Material: Slides, Self-study tutorial, Youtube Playlist

Speaker

John Chilton

Web Requests

Video Length: 35m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: TODO
Training Material: Slides, Self-study tutorial, Youtube Playlist

Speaker

John Chilton

app and Dependency Injection

Video Length: 15m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: TODO
Training Material: Slides, Self-study tutorial, Youtube Playlist

Speaker

John Chilton

Models and Managers

Speaker

John Chilton

Pluggable Components

Video Length: 45m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: TODO
Training Material: Slides, Self-study tutorial, Youtube Playlist

Speaker

John Chilton

Web Client

Speaker

John Chilton

Supporting Materials

Slides: Galaxy Architecture
Self-study tutorial: Contributing to Galaxy Core
Youtube Playlist: Always contains the latest version of these lectures.
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Slack channel: #dev-galaxy-core - Have question about the training? Did you run into a problem? Just wanna chat? Ask an Instructor on Slack!
Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: #dev-galaxy-core ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet (hashtag #usegalaxy), and follow the GTN on Twitter! @gxytraining

Instructors

The following instructors are available online this week for support for this session:

John Chilton

The Global GTN Community

Hall of Fame

Self-Study Galaxy Development

These tutorials don’t have video walkthroughs, but will all be supported by their authors during the week. So please work through these tutorials by yourself, and ask LOTS of questions in Slack!

Self-Study Tutorial

Ever wondered how to interact with the Galaxy API to scale your work and automated processes? Learn how to here with BioBlend.

This tutorial consists of a set of hands-on exercises in the form of Jupyter Notebooks. You can run these locally on your computer, or online via Binder. See the README in the tutorial listed below for more information.

Supporting Materials

Slides: Scripting Galaxy using the API and BioBlend
Tutorial: Jupyter Notebook Bioblend Tutorials
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Slack channel: dev-bioblend - Have question about the training? Did you run into a problem? Just wanna chat? Ask an Instructor on Slack!
Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: dev-bioblend ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet (hashtag #usegalaxy), and follow the GTN on Twitter! @gxytraining

Instructors

The following instructors are available online this week for support for this session:

Nicola Soranzo

Earlham Institute

Catherine Bromhead

University of Melbourne

Simon Bray

The Global GTN Community

Hall of Fame

Self-Study Tutorial

This tutorial will teach you how to contribute to BioBlend and add support for a Galaxy API in BioBlend.

Supporting Materials

Tutorial: Contributing to BioBlend Development
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Slack channel: dev-bioblend - Have question about the training? Did you run into a problem? Just wanna chat? Ask an Instructor on Slack!
Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: dev-bioblend ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet (hashtag #usegalaxy), and follow the GTN on Twitter! @gxytraining

Instructors

The following instructors are available online this week for support for this session:

Nicola Soranzo

Earlham Institute

rikeshi

Catherine Bromhead

University of Melbourne

Simon Bray