Setting up a dev Onedata instance

Overview
Questions:

How to set up a minimal Onedata dev instance?

How can I test the Galaxy & Onedata integration in a sandbox environment?

Objectives:

Quickly set up a zero-config dockerized Onedata deployment.

Run Onedata locally for Galaxy development and testing purposes.

Requirements:

tutorial Hands-on: Getting started with Onedata distributed storage

Time estimation: 20 minutes

Level: Introductory Introductory

Supporting Materials:

FAQs

Published: Mar 24, 2025

Last modification: Mar 24, 2025

License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MIT

version Revision: 1

Prerequisites

It’s recommended that you have basic knowledge about Onedata. If needed, follow this tutorial first!

Introduction

If you are familiar with docker, you can easily set up a local Onedata sandbox deployment. It may come in handy if you wish to test Galaxy & Onedata integration or develop features related to data management in Galaxy.

Demo mode

Use the official Onedata tutorial for running the system in demo mode.

If you are new to this, run a Onezone and Oneprovider instance in foreground. When the setup is finished, log in to the Onezone interface, using the IP address and credentials displayed in Onezone docker logs (as explained in the guide).

Use the Onezone docker IP as the Onezone domain in all Onedata related configs in Galaxy. Use the predefined Space called demo-space for Storage Location configs (global or BYOS).

Warning: The demo mode runs on self-signed certificates

You will need to accept the untrusted connection in your browser to enter the UI.

Remember to disable TLS certificate validation in the Galaxy configs!

Follow the getting started tutorial to acquire an access token, or use the convenience scripts of the demo mode (as explained in the guide).

The demo mode is used for setting up Onedata in Galaxy’s Object Store integration tests. Take a look at the code (search for “onedata”).

You've Finished the Tutorial

Key points

A local Onedata deployment can be easily set up using the dockerized “demo mode”.

You may set up Onedata and use the sandbox credentials to connect it to Galaxy.

A local Onedata deployment may be useful to test your changes to the data-related logic of Galaxy.

Frequently Asked Questions

Have questions about this tutorial? Have a look at the available FAQ pages and support channels

Feedback

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Citing this Tutorial

Łukasz Opioła, Setting up a dev Onedata instance (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/dev/tutorials/onedata-dev-instance/tutorial.html Online; accessed TODAY
Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

@misc{dev-onedata-dev-instance,
author = "Łukasz Opioła",
	title = "Setting up a dev Onedata instance (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/dev/tutorials/onedata-dev-instance/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}
}

                   

Congratulations on successfully completing this tutorial!

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/dev/tutorials/onedata-dev-instance/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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