Comment: Note to contributors

• Work in progress!! First draft to try to get a structure to make sense.
• Needs many contributors to make it useful. What would you like to have known, when you first tried getting things done in Galaxy? Please add what’s missing and fix what’s broken. Headings are mostly stubs waiting to be edited and extended
• Trying to describe the big picture will necessarily be big. Will probably need to break this already very wordy module into separate parts.
• Add your story or stories to the stories tutorial too please!
• Ross has strong opinions.
• Many of them are probably wrong but he doesn’t know which ones yet.
• Please feel free to contribute your own, to make this more useful to future readers.

Comment: Note to readers

• This module introduces the most important resouces of the Galaxy project. They are grouped arbitrarily and there are many overlaps, because Galaxy grows organically through collaborations, rather than by design.
• The project continues to expand rapidly, so this module will need updating regularly
• The Hub provides much more detail about many of the same structures and their activities, but this material is designed to provide simplified views of the project, so the Hub becomes easier to navigate.
• This is an attempt at a kind of field guide to the ecosystem generating those Hub activities, for the use of participants trying to navigate it.

Agenda: Field Guide part 2. Resources in Galaxy.

1. 2. Resources for the Galaxy project
   1. Source code
   2. Computational infrastructure, support and analysis services
   3. Collaborating grants
   4. Community contributors
   5. Further reading

2. Resources for the Galaxy project

The project is complicated, because in addition to all the people and their interactions described in a companion lesson, it requires grant and hardware allocations, together with skilled personnel, to provide services and to manage code assets, communities and other essential corporate functions for a complex global enterprise.

• Large scale research computating infrastructure is utilised at each of the usegalaxy.* sites.
• A funded team of dedicated professional staff are needed to provide highly available services.
• The team also manages core code assets and supports community contributors fixing bugs and adding additional value.
• Galaxy code depends on many other open source communities.

Source code

• Many other open source communities provide:
  • Galaxy source code dependencies
  • Command line analysis repositories for tools
• Without these, Galaxy could not exist.
• Github committers and community
• The core framework code, markup for the Hub and GTN, and related resources are also maintained on GitHub, allowing automated testing for pull requests, and independent review before changes are accepted.

Computational infrastructure, support and analysis services

“Free” user allocations for storage and computing depend on the available resources and the intensity of user demand. They are sufficient for many common data intensive projects, but are not suitable for very large data or extremely demanding computing because availability is limited to the resources provided by collaborators and it is far from infinite.

Each of the main usegalaxy.* services shares the main source code, and system administrators share their skills, but they each involve a different set of hardware and storage, so there are important differences in the fine detail of deployment.

• Australia
• Europe
• USA

Collaborating grants

• Would PI’s want to advertise their deliverables here?
• One way of letting potential collaborators know what you’re doing?
• Does not need budgets :)
• AnVIL
• Cancer….
• Your ideas here please?

Community contributors

• Very important resource
• Bug fixes, ideas…

Further reading

For more on the main components, and stories of how people get things done in the project, choose from the other lessons in this Topic:

• Introductory material
• People and their interactions
• Project outputs and deliverables
• Community development success stories

Key points

• Galaxy is a complicated, participatory self-governing collaborative community project

• Participants engage with the project on their own individual terms

• Multiple perspectives and opinions are needed to see the whole interacting structure

• Vision: Build hard features like reproducibility into an analysis framework with pluggable tools

• Running code as a free service provides effective stress testing for software defects and useability

• Project depends on and collaborates as part of the open science ecosystem

• Started in genomics but now adapted to suit many data rich disciplines

• New contributors and investigators are highly valued and warmly welcomed

Frequently Asked Questions

Feedback

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Citing this Tutorial

1. ggsc, Ross Lazarus, Resources used by the Galaxy project. WIP! Mostly stubs. Help wanted (Galaxy Training Materials). http://0.0.0.0:4000/training-material/topics/galaxy-project/tutorials/resources/tutorial.html Online; accessed TODAY
2. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{galaxy-project-resources,
author = "ggsc and Ross Lazarus",
title = "Resources used by the Galaxy project. WIP! Mostly stubs. Help wanted (Galaxy Training Materials)",
year = "",
month = "",
day = ""
url = "\url{http://0.0.0.0:4000/training-material/topics/galaxy-project/tutorials/resources/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} Computational Biology}
}

                   

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 http://localhost:4000//training-material//api/topics/galaxy-project/tutorials/resources/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

--- {}