Upload data to Galaxy

Under Development!

This tutorial is not in its final state. The content may change a lot in the next months. Because of this status, it is also not listed in the topic pages.

Authors:

Bérénice Batut

Overview
Questions:

How to upload data to Galaxy

Objectives:

Learn how to upload a file by pasting in a URL

Learn how to import data from a shared library

Determine the best strategy to get data into Galaxy

Time estimation: 40 minutes

Level: Introductory Introductory

Supporting Materials:

instances Available on these Galaxies

Possibly Working

UseGalaxy.eu

UseGalaxy.org

UseGalaxy.org.au

Containers

docker_image Docker image

Last modification: Nov 3, 2023

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

purl PURL: https://gxy.io/GTN:T00185

version Revision: 6

There are several ways to get data into Galaxy:

Uploading a file by pasting in a URL
Uploading a file from the computer
Uploading using a FTP server
Import an entire history
Import data from a shared library
…

Agenda

Upload a file via an URL

Import from a shared library

Upload a file via an URL

Hands-on: Data upload from URL
Create a new history

Click the new-history icon at the top of the history panel.

If the new-history is missing:

Click on the galaxy-gear icon (History options) on the top of the history panel

Select the option Create New from the menu
Copy the following URL
https://zenodo.org/record/582600/files/mutant_R1.fastq
Import it in the history

Copy the link location

Click galaxy-upload Upload Data at the top of the tool panel

Select galaxy-wf-edit Paste/Fetch Data

Paste the link(s) into the text field

Press Start

Close the window

Import from a shared library

Hands-on: Data upload from URL
Create a new history

Click the new-history icon at the top of the history panel.

If the new-history is missing:

Click on the galaxy-gear icon (History options) on the top of the history panel

Select the option Create New from the menu
Copy the following URL
https://zenodo.org/record/582600/files/mutant_R1.fastq
Import it in the history

Copy the link location

Click galaxy-upload Upload Data at the top of the tool panel

Select galaxy-wf-edit Paste/Fetch Data

Paste the link(s) into the text field

Press Start

Close the window

Key points

There are several ways to get data into Galaxy

you can upload a file by pasting in a web address, you can upload a file from your computer, and you can import an entire history.

Frequently Asked Questions

Have questions about this tutorial? Check out the FAQ page for the Introduction to Galaxy Analyses topic to see if your question is listed there. If not, please ask your question on the GTN Gitter Channel or the Galaxy Help Forum

Feedback

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Citing this Tutorial

Bérénice Batut, Upload data to Galaxy (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/introduction/tutorials/dummy/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{introduction-dummy,
author = "Bérénice Batut",
	title = "Upload data to Galaxy (Galaxy Training Materials)",
	year = "",
	month = "",
	day = ""
	url = "\url{https://training.galaxyproject.org/training-material/topics/introduction/tutorials/dummy/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}
}

                   

Congratulations on successfully completing this tutorial!

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/introduction/tutorials/dummy/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: []