Welcome everybody, and thank you for joining the GCC training week!

Everything you need for this course can be found on this webpage. More information including links to all training materials can be found by clicking on each session.



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Welcome & Practical Information

Self-Study Tutorial

Start here; we will go over all the important things to know to get the most out of this workshop

Supporting Materials

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

Here are the tasks you need to do ….

Supporting Materials

  • Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack!
  • 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, and follow the GTN on Twitter! @gxytraining
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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.

Speaker

galaxycommunity
The Global Galaxy Community

Supporting Materials

GTN logo

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

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

Speaker

nsoranzo
Nicola Soranzo
rikeshi
rikeshi

Supporting Materials

  • Tutorial: Contributing to BioBlend Development
  • Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack!
  • 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, and follow the GTN on Twitter! @gxytraining
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Tutorial

Video Length: 2m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: Here you will creating Galaxy tools from scratch using Conda for requirements, Planemo for testing, and Git for deployment.

Speaker

Supporting Materials

GTN logo

Instructors

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

Tutorial

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: Here you will creating Galaxy tools from scratch using Conda for requirements, Planemo for testing, and Git for deployment.

Speaker

Supporting Materials

GTN logo

Instructors

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

Tutorial

Video Length: 41m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: Here you will creating Galaxy tools from scratch using Conda for requirements, Planemo for testing, and Git for deployment.

Speaker

bernt-matthias
bernt-matthias

Supporting Materials

GTN logo

Instructors

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

Tutorial

Video Length: 30m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: Here you will creating Galaxy tools from scratch using Conda for requirements, Planemo for testing, and Git for deployment.

Speaker

Supporting Materials

GTN logo

Instructors

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

Tutorial

Video Length: 3m
Subtitles By: The Global Galaxy Community
Description: Here you’ll get a quick overview about what the ToolFactory is and how it works.

Speaker

awspolly
These slides are narrated by AWS Polly.

Supporting Materials

GTN logo

Instructors

The following instructors are available online this week for support for this session:
fubar2
Ross Lazarus

Tutorial

Video Length: 7m
Subtitles By: Ross Lazarus
Description: Here you’ll see how the ToolFactory works and get a quick tour of the hands on

Speaker

awspolly
These slides are narrated by AWS Polly.

Supporting Materials

GTN logo

Instructors

The following instructors are available online this week for support for this session:
fubar2
Ross Lazarus

Tutorial

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: Why this training might be useful: If you write useful scientific analysis scripts, but have not yet learned to create new tools for Galaxy, the ToolFactory might help. It generates the XML “wrapper” for any simple, working command line script. The script, I/O and parameters are specified using a Galaxy tool form. When the form is completed, the tool it specifies is generated and installed, ready to run in the local Galaxy server. If a generated tool might be useful to other users, it can be linted and tested, producing a toolshed-ready archive for sharing. Training model and support: The ToolFactory training is designed for asynchronous self guided study. Developers have widely varying needs and interests. The ToolFactory is adaptable to almost any of these if a script is ready to wrap. No formal presentations are planned but the developer will be available during designated sessions to answer questions and learn about new bugs. Resources:
  1. Hello Galaxy video demonstration 10m (TBA)
  2. Tutorial: “hello Galaxy” tools
  3. Tutorial: Advanced features
  4. Sample tools in the Appliance history: The best way to learn what the ToolFactory can do is to rerun them with changes to the script, I/O and parameters to suit your needs.
  5. The ToolFactory Appliance is a flavour of docker-galaxy-stable for your private workstation or high-end laptop. Installation and disposal are described in the introductory tutorial.
Prerequisites: Linux shell and scripting skills are required. A dedicated, private Linux workstation or high-end laptop is needed for Appliance installation. The ToolFactory is recommended for private desktop use only because executing unrestricted user installed tools is an unacceptable potential security risk for any production server.

Speaker

fubar2
Ross Lazarus

Supporting Materials

GTN logo

Instructors

The following instructors are available online this week for support for this session:
fubar2
Ross Lazarus

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.

Speaker

Nicola Soranzo

Nicola Soranzo

Earlham Institute

Supporting Materials

  • Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack!
  • 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, and follow the GTN on Twitter! @gxytraining
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Self-Study Tutorial

Speaker

Saskia Hiltemann

Saskia Hiltemann

Erasmus Medical Center

Speaker

Bérénice Batut

Speaker

Helena Rasche

Helena Rasche

Avans Hogeschool

Speaker

Simon Gladman

Simon Gladman

University of Melbourne

Supporting Materials

  • Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack!
  • 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, and follow the GTN on Twitter! @gxytraining
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Self-Study Tutorial

Speaker

Dannon Baker

Supporting Materials

  • Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack!
  • 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, and follow the GTN on Twitter! @gxytraining
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Galaxy Core Development

This covers everything you need to start developing for Galaxy, understanding the codebase, adding APIs, implementing features. This module will likely take you several days to complete.

Self-Study Tutorial

Speaker

John Chilton

John Chilton

Penn State University

Speaker

Nate Coraor

Nate Coraor

Penn State University

Speaker

Dannon Baker

Supporting Materials

  • Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack!
  • 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, and follow the GTN on Twitter! @gxytraining
GTN logo

Self-Study Tutorial

Speaker

Sergey Golitsynskiy

Sergey Golitsynskiy

Johns Hopkins University

Speaker

Assunta DeSanto

Assunta DeSanto

Penn State University

Speaker

John Chilton

John Chilton

Penn State University

Speaker

Marius van den Beek

Marius van den Beek

Penn State University

Supporting Materials

  • Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack!
  • 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, and follow the GTN on Twitter! @gxytraining
GTN logo

Self-Study Tutorial

Speaker

John Chilton

John Chilton

Penn State University

Speaker

Dannon Baker

Speaker

Sergey Golitsynskiy

Sergey Golitsynskiy

Johns Hopkins University

Speaker

Assunta DeSanto

Assunta DeSanto

Penn State University

Speaker

Marius van den Beek

Marius van den Beek

Penn State University

Supporting Materials

  • Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack!
  • 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, and follow the GTN on Twitter! @gxytraining
GTN logo

Self-Study Tutorial

Here you can pick a Galaxy bug that you find interesting, especially a ‘paper-cut’, and the instructors will help guide you to resolving this bug.

Supporting Materials

  • Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack!
  • 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, and follow the GTN on Twitter! @gxytraining
GTN logo



Acknowledgements

This Global Galaxy course is only possible thanks to a Global network of instructors and institutes.

Presenters & Instructors & Facilitators & Community Caption Contributors

ddan
Dinh Duy An Nguyen
shiltemann
Saskia Hiltemann
andrewr
Andrew Rajczewski
nsoranzo
Nicola Soranzo
pvanheus
Peter van Heusden
cat-bro
Catherine Bromhead
ennovytje
Yvonne Hiltemann
galaxycommunity
The Global Galaxy Community
mvdbeek
Marius van den Beek
assuntad23
Assunta DeSanto
blankenberg
Daniel Blankenberg
jvanbraekel
Julien Van Braekel
fpsom
Fotis E. Psomopoulos
jennaj
Jennifer Hillman-Jackson
nekrut
Anton Nekrutenko
delphine-l
Delphine Lariviere
fubar2
Ross Lazarus
miaomiaozhou88
Miaomiao Zhou
abretaud
Anthony Bretaudeau
malloryfreeberg
Mallory Freeberg
timothygriffin
Timothy J. Griffin
nomadscientist
Wendi Bacon
hexylena
Helena Rasche
rwinand
Raf Winand
kmurat1
Katarzyna Kamieniecka
MariaTsayo
Maria Tsagiopoulou
annefou
Anne Fouilloux
willemdek11
Willem de Koning
davelopez
David Lopez
ic4f
Sergey Golitsynskiy
eancelet
Estelle Ancelet
kpoterlowicz
Krzysztof Poterlowicz
s3by01
Sébastien Fouilloux

Institutions

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