The Community lab, a centralised webpage that enables communities to rapidly aggregate, curate, integrate, display, and launch relevant tools, workflows, and training on different Galaxy servers. This user-friendly interface, built on the Galaxy framework, provides community members with data analysis capacity without requiring programming expertise. Users can run individual tools or create complex workflows, with full provenance tracking to ensure reproducibility, designed specifically for the community research (Nasr et al., 2024). For example, the microgalaxy lab (Europe).

The aim of this tutorial is to create the files necessary to display the labs in each Galaxy instance.

You can also use the Galaxy Labs engine.

Agenda

In this tutorial, we will cover:

1. Create the lab specific files (automatic)
2. Modify the generated files to personalize your community lab
3. Create community specific sections to personalize your community lab
4. Include the labs in the different instances
5. Conclusion

Create the lab specific files (automatic)

The labs are composed of various files, some that are specific to your community and some that are common between all the labs. To automatically create the necessary files from a set of templates, a script was generated (“sources/bin/populate_labs.sh)

This script will create the following structure and files: communities//lab/ CONTRIBUTORS README.md base.yml conclusion.html intro.html usegalaxy.eu.yml usegalaxy.fr.yml usegalaxy.org.yml

communities//lab/sections_templates/ 1_data_import_and_preparation.yml 2_tools.yml 3_workflows.yml 4_tutorials.yml 5_support_and_help.yml 6_community.yml

The files are created and updated automatically using GitHub actions, you just need to add a bit of code to point to your community folder.

Hands On: Generate the files using Github Actions

1. Go to the Galaxy Codex repo
2. Go to the file .github/workflows/fetch_filter_resources.yaml
3. On the right, click on the pen to “Edit this file”
4. Scroll down

5. Duplicate the section called “Populate Lab"

     - name: Populate <community-name> Lab
       run: |
         bash sources/bin/populate_labs.sh
       env: 
         COMMUNITY: <community-name>
   

6. Replace <community-name> by the name of your community
7. Commit changes the changes to a new branch that you name “new lab for [Community-name]”

After that, your commit will be reviewed (and approved) by admins. On the following Sunday (or upon request), this action will be launched and will create the new files in the appropriate community folder (communities/<your community>/lab/).

Modify the generated files to personalize your community lab

Once the files are created, you should update them as some contain template text that are not community specific.

Files to update :

• communities/<your community>/lab/CONTRIBUTORS –> Add the handles of everyone who contributed in the lab
• communities/<your community>/lab/README.md –> Change all <your-community> by your community name
• communities/<your community>/lab/base.yml –> Change all <your-community> by your community name
• communities/<your community>/lab/intro.html –> Include a description of your community.

Files that do not require a manual update :

• “communities//lab/conclusion.html" --> No change required.
• “communities//lab/sections/*" --> No change required.

The files in the section folders contain the code for each table visible in the lab. You can check different labs for inspiration, such as the microgalaxy lab.

Create community specific sections to personalize your community lab

If you want additional sections, for example, the “Microbial isolates” and “Microbiome” sections in the microgalaxy lab.

Hands On: Add community specific sections

1. Find an appropriate template. You can use other files in your section folder, or browse other labs, such as microgalaxy lab code, and copy the raw code as a template.
2. Create the file in your section folder. Name it with a digit (numerical order) and a descriptive name (i.e. “7_microbial_isolate”).
3. Copy the raw code in this newly created file.
4. Update the code to display what you want.
5. Save the file.
6. Open communities/<your community>/lab/base.yml
7. Add the previously created file in the sections (see microgalaxy base file for example)
8. Save communities/<your community>/lab/base.yml
9. Commit the changes, create the pull request (if not done previously)

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

Include the labs in the different instances

For the lab to be accessible from the different instances, you need to add files in each instance independently.

For the French instance (https://usegalaxy.fr), all the steps are described in Issue 297. You can use the merge request done for the biodiversity lab as a reference.

For the European instance (https://usegalaxy.eu), this tutorial will be updated later. You can use the pull request done for the biodiversity lab as a reference.

For the American instance (https://usegalaxy.org), this tutorial will be updated later. You can use the pull request done for the biodiversity lab as a reference.

For the Australian instance (https://usegalaxy.org.au), this tutorial will be updated later. You can use the pull request done for the biodiversity lab as a reference.

Conclusion

You now have all the files necessary to display your lab in several instances and they should soon be available to your users.

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• The Community lab is a centralised webpage built on the Galaxy framework that enables communities to use specific tools, workflows and tutorials on different Galaxy servers.

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 the labs in the different Galaxy instances for your community (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/community/tutorials/community-lab/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-lab,
author = "Bérénice Batut and Paul Zierep and Solenne Correard and Keiler Collier",
	title = "Creation of the labs in the different Galaxy instances for your community (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/community/tutorials/community-lab/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-lab/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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