This tutorial covers how to set up a subdomain on usegalaxy.eu. We will take here the example of the earth system subdomain and follow the step one by one.

Agenda

In this tutorial, we will cover:

1. Add your subdomain on a Galaxy server
2. Enable the interactive tools
3. Make a nice tool panel (only for interactive tools)
4. Customize the front page
5. Let people know
6. Conclusion

Add your subdomain on a Galaxy server

Hands-on: Subdomain name

• Clone the Github repository of the Galaxy server (of where you want your subdomain to be attached)
• For Galaxy europe clone the Infrastructure repo
• Create a branch on your fork
• Open the file dns.tf and edit it
• You should add the name of your subdomain to the list my_new_and_shiny_subdomain.usegalaxy.eu or for the example here earth-system.usegalaxy.eu AND update count (number of subdomains) as shown below.

• Then commit your changes and write a nice message for the admin when you open your Pull Request.

Enable the interactive tools

Hands-on: Galaxy Interactive Tool

• Clone the Github repository of the Galaxy server (of where you want your subdomain to be attached)
• For Galaxy europe clone the Infrastructure-playbook repo
• Create a branch on your fork
• Open the file sn06.yml and edit it
• You should add the name of your subdomain to the list “.my_new_and_shiny_subdomain.usegalaxy.eu” or for the example here “.earth-system.usegalaxy.eu”
• AND add “*.interactivetoolentrypoint.interactivetool.earth-system.usegalaxy.eu” as shown below.

• Then commit your changes and write a nice message for the admin when you open your Pull Request.

Hands-on: Add the interactive tool section to the tool panel

• First, on your Infrastructure-playbook fork, create a new branch
• Go to templates/galaxy/config/
• Open the file global_host_filters.py.j2 and edit it
• In the function per_host_tool_labels add your subdomain as followed

  if "earth-system.usegalaxy.eu" in host:
    return label.id in valid_labels"
  

• Then in the DOMAIN_SECTIONS add the the interactive tool section (this will allow to see on the subdomain interface the tool section “Interactive tools”) as folowed: 'earth-system': ["interactivetools"],

• Second, on the same fork go to files/traefik/rules/

• Open and edit template-subdomains.yml, there you need to add the folowing line for your subdomain ``

• Finally, commit all your changes and write a nice message for the admin when you open your Pull Request.

Make a nice tool panel (only for interactive tools)

Hands-on: Customize the tool panel (only for the interactive tools)

• On your Infrastructure-playbook fork (don’t forget to synchronize it)
• First, go to templates/galaxy/config/
• Open the file tool_conf.xml.j2 and edit it

• From there you can create your own tool sections where your different interactive tools can be organized. See the example of earth-system below.

• Then, commit your changes

• Secondly, still in templates/galaxy/config/
• Open the file global_host_filters.py.j2 and edit it

• Add the different new sections of tools created to your subdomain and prevent those new sections to appear in any other subdomain as shown below.

• Then commit your changes and write a nice message for the admin when you open your Pull Request.

Customize the front page

Hands-on: Update the homepage

• For Galaxy europe clone the website repo
• Create a branch on your fork
• Create an index file in markdown for instance “index-earth-system.md”
• Once created let your imagnination flows to make the looks and feel of your homepage (if needed here is a PR example)

• If you want to add images to your front page add them as folowed assets/media/my_incredidle_image.png

• Then commit your changes, write a nice message for the admin when you open your Pull Request. If in the future you want to change the front page just update the index file.

Tip: Add a custom welcome.html

There is also the possibility to add a custom welcome.html, as well as other custom static files like the singlecell subdomain did

Hands-on: Add a theme

• On your Infrastructure-playbook fork (don’t forget to synchronize it)
• Go to group_vars/sn06/
• Open the file subdomains.yml and edit it. There you have to add the name of your subdomain.
• In this same file you can also customize a theme for your subdomain.

Let people know

Hands-on: Make some communication on your new subdomain

• Clone the galaxy-hub repo
• Create a branch on your fork
• In content/news create a folder for your news example “2023-10-17-earth-system” and in it create an index.md file

• In this index file write your blog post don’t hesitate to add some nice photos

• Then commit your changes and open your Pull Request.

Conclusion

Your Subdomain is ready to be used !

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• Subdomain

• Community

• Earth System

Frequently Asked Questions

Feedback

Did you use this material as an instructor? Feel free to give us feedback on how it went.
Did you use this material as a learner or student? Click the form below to leave feedback.

Citing this Tutorial

1. Marie Josse, Create a subdomain for your community on UseGalaxy.eu (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/admin/tutorials/subdomain/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{admin-subdomain,
author = "Marie Josse",
	title = "Create a subdomain for your community on UseGalaxy.eu (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/admin/tutorials/subdomain/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}
}

                   

Funding

These individuals or organisations provided funding support for the development of this resource

Gallantries

This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.

Fair-Ease

FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.

EuroScienceGateway

EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.

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/admin/tutorials/subdomain/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: []

Feedback

No feedback has been recieved yet for this training. Be the first one by filling in the feedback form from above.