Exporting to Onedata remote

Overview
Questions:

How to export Galaxy datasets to Onedata?

What configuration is needed for Onedata export?

What permissions are required for Onedata export?

Objectives:

Configure a writable Onedata Remote File Source.

Learn how to export datasets to Onedata.

Understand the requirements for Onedata export.

Requirements:

tutorial Hands-on: Galaxy Basics for genomics

tutorial Hands-on: Downloading and Deleting Data in Galaxy

tutorial Hands-on: Getting started with Onedata distributed storage

tutorial Hands-on: Importing (uploading) data from Onedata

Time estimation: 5 minutes

Level: Introductory Introductory

Supporting Materials:

FAQs

instances Available on these Galaxies

Possibly Working

UseGalaxy.eu

UseGalaxy.org

UseGalaxy.org.au

UseGalaxy.fr

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

This tutorial assumes that you have basic knowledge about Onedata and access to a Onedata ecosystem. If needed, follow this tutorial first!
To use Onedata as a remote file source for data export, you need the domain of the Onezone service and a suitable access token. Here is the relevant guide on how to get them.
The Galaxy server must be properly configured by the admins for the Onedata remote and/or Onedata BYOD templates to be available. Here is the corresponding tutorial.

Introduction

Onedata Remote File Source can be configured as writable. In such a case, you can export your Galaxy datasets to a Onedata Space.

Configuration

Follow the same steps as in the Importing (uploading) data from Onedata tutorial to configure a Onedata Remote File Source.

Make sure that the Remote File Source is writable. In case of you own, it’s as simple as checking the toggle in the configuration. In case of generic remotes, it’s in the hands of admins to mark the Onedata remote as writable.

Exporting datasets

Follow these steps:

Find the Export datasets to remote files source tool in the toolbox.
Choose the dataset to be exported and choose your Onedata Remote File Source in the Directory URI section.
Adjust the configuration if needed.
Run the tool.
Check your Onedata account to find the exported dataset at the specified path.

Troubleshooting

In case of errors:

Check the section Use distributed compute resources in the Manage Information section of the Preferences menu. It’s possible that the specific Pulsar endpoint is unable to run the job. Try using the default settings.
Avoid whitespace characters (spaces, tabs) in the Directory URI, as they are known to cause problems.
Take a look at the troubleshooting guide.

The Onedata Remote file source can also be used for data import — see the tutorial.

You've Finished the Tutorial

Key points

Export can be done through the “Export datasets” tool.

Remote File Source must be configured as writable to enable export.

Write access is required in the Onedata access token.

Export works with both generic and user-configured Remote File Sources.

Frequently Asked Questions

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

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Citing this Tutorial

Łukasz Opioła, Bartosz Walkowicz, Exporting to Onedata remote (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/onedata-remote-export/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{galaxy-interface-onedata-remote-export,
author = "Łukasz Opioła and Bartosz Walkowicz",
	title = "Exporting to Onedata remote (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/onedata-remote-export/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/galaxy-interface/tutorials/onedata-remote-export/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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