This tutorial explains how to make your brand new tools, once they’re published through a Pull Request (check this tutorial on how to build your tool from scracth), visible on your subdomain. Here we’ll follow the example on how to make the tools visible on Galaxy for earth System. You can also find the explanations on how to add your tools on this Github page.

Agenda

In this tutorial, we will cover:

1. Add your batch tool to the right section
2. Add a section of tools to your subdomain
3. Add you interactive tool to the right section
4. Conclusion

Add your batch tool to the right section

Hands-on: Tool sections (for batch tools)

• Clone the Github repository of the Galaxy server (of where your subdomain to be attached)
• For Galaxy Europe, fork the usegalaxy-eu-tools repo
• Create a branch on your fork
• Browse through the different yaml files and select the one that correspond to your subdomain for earth system everything is made under the ecology owner. The name of the files corresponds to a toolshed owner or community and a few of those communities with a review system and CI integration gets special trust and auto-updates.
• Once in the yaml you can add the section for your tool (you want to know what are the existing tool sections ? Go check the categories defined here)

An example on how to fill in the yaml file

- name: id_of_your_tool
  owner: choose_the_owner_relative_to_a_github_repo
  tool_panel_section_label: 'Choose the section where your tool belongs'

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

This part is only to make batch tool visible in your subdomain.

Add a section of tools to your subdomain

Hands-on: Sections for your subdomain

• If not already done clone the Galaxy Europe Infrastructure-playbook repo
• Create a branch on your fork
• Go to the file global_host_filters.py.j2 in templates/galaxy/config/
• Open it and edit it the “DOMAIN_SECTIONS” part go to your subdomain line and in the list of section add the one you need for instance "climate_analysis"

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

Add you interactive tool to the right section

Hands-on: Interactive tool sections

• If not already done clone the Galaxy Europe Infrastructure-playbook repo
• Create a branch on your fork
• Go to the file tool_conf.xml.j2 in templates/galaxy/config/
• Open it and edit it by adding the xml file of the interactive tool to the section interactive tool or any other interactive tool section (to know more on how to create your interactive tool section folow this tutorial)
• Below an example of how to add the interactive tool panoply to the earth system subdomain.

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

If you choose to create a new section for your interactive tool don’t forget add this section to your subdomain !

Conclusion

You can now start to build your workflow on your subdomain !

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• Subdomain

• Tool panel

• Interactive tools

Frequently Asked Questions

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Citing this Tutorial

1. Marie Josse, Make your tools available on your subdomain (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/community/tutorials/tools_subdomains/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-tools_subdomains,
author = "Marie Josse",
	title = "Make your tools available on your subdomain (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/community/tutorials/tools_subdomains/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/community/tutorials/tools_subdomains/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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