Similarly to the numerous tools available on Galaxy, the Galaxy Training Network includes numerous tutorials. This tutorial will take you through the steps to generate resources listing all the relevant tutorials and display the tutorial table on your community codex page.

The pipeline creates a table with all the tutorials. This table can be filtered to only include tutorials that are relevant to a specific research community.

The generated community-specific table can be used as is (e.g. downloadable tsv file) and/or embedded (e.g. into a Galaxy Hub page or Galaxy subdomain).

The pipeline is fully automated and executes on a weekly basis. Any research community can apply the pipeline to create a table specific to their community.

The aim is this tutorial is to create a tutorial table for a community.

Agenda

In this tutorial, we will cover:

1. Add your community to the Galaxy CoDex
2. Pull list of tags relevant to your community
3. Add the list relevant tags for your community in the tutorial_tags file
4. Embed the table in your community page on the Hub
5. Conclusion

Add your community to the Galaxy CoDex

You first need to check if your Community is in the Galaxy CoDex, a central resource for Galaxy communities. If the community is already there, you can move to the next step of this tutorial.

If you community is not already included, follow this step :

Hands On: Add your community to the Galaxy CoDex

You need to create a new folder in the data/community folder within Galaxy CoDex code source.

1. If not already done, fork the Galaxy Codex repository
2. Go to the communities folder
3. Click on Add file in the drop-down menu at the top
4. Select Create a new file
5. Fill in the Name of your file field with: name of your community + /metadata/tutorial_tags This will create a folder for your community, a new folder for your community called metadata and a file called tutorial_tags.
6. Click on Commit changes
7. Fill in the commit message with something like Add X community
8. Click on Create a new branch for this commit and start a pull request
9. Create the pull request by following the instructions

Pull list of tags relevant to your community

To add tutorials in your community tutorial table, you will need to indicate a list of tags relevant to your community, and tutorials associated with this tag will be automatically pulled from the Galaxy Training Network one a week. Only tutorials with the selected tags will be added to the filtered table. You will then be able to remove tutorials that are not relevant to your community or deprecated.

Hands On: Select tutorials tags from the Galaxy Training Network

1. Go to the Galaxy Training Network
2. Browse for tutorials that are relevant to your community
3. Note the tags that are associated with tutorials of interest

Comment: Tips

You can also create a tag (for example, your community name) and tag all relevant tutorials with it. Then, you only need to use this tag to pull all the relevant tutorials.

Add the list relevant tags for your community in the tutorial_tags file

Hands On: Add the relevant tags to the tutorial_tags file

1. Open or create a file named tutorial_tags in your comunity metadata folder (communities/<your community>/metadata/tutorial_tags)

2. Add the name of the tags relevant to your community in the tutorial_tags file, with 1 tag per row (See above for how to identify the appropriate tags)

   For example:

   Assembly
   Metagenomics
   

Once you have a list of the tags that you wish to keep, you can submit this to Galaxy CoDex.

Hands On: Submit the new list of tags to Galaxy CoDex

1. Click on Commit changes at the top
2. Fill in the commit message with something like Add tutorials tags for my community
3. Click on Create a new branch for this commit and start a pull request
4. Create the pull request by following the instructions

The Pull Request will be reviewed. Make sure to respond to any feedback.

On the sunday following the Pull Request merge, a table with all tutorial will be created in communities/<your community>/resources/tutorials.tsv

Here is an overview of the files :

Open image in new tab

Embed the table in your community page on the Hub

The table you have created can be embedded in your community page on the Hub, e.g. microGalaxy.

Hands On: Embed your table

1. If not already done, fork the repository Galaxy Hub
2. Open or create your community page: content/community/sig/<your community>/index.md
3. TO DO : We Will soon update this section to explain how to include the table, sorry for the inconvenience.
4. Submit the changes
5. Wait for the Pull Request to be merged

Conclusion

You now have a table with tutorials available for your community, and this table is embedded in a community page.

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• The Galaxy Codex extracts all Galaxy tutorials to create tables

• The community Galaxy tutorials table can be embedded into any website

Frequently Asked Questions

• Topic FAQs
• Galaxy FAQs
• GTN Matrix Chat
• Galaxy Help Forum

Feedback

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Citing this Tutorial

1. Bérénice Batut, Paul Zierep, Solenne Correard, Keiler Collier, Creation of a Galaxy tutorial table for your community (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/community/tutorials/community-tutorial-table/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{community-community-tutorial-table,
author = "Bérénice Batut and Paul Zierep and Solenne Correard and Keiler Collier",
	title = "Creation of a Galaxy tutorial table for your community (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/community/tutorials/community-tutorial-table/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/community/tutorials/community-tutorial-table/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

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