Introduction

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

1. Introduction
2. Upload a file via an URL
3. Import from a shared library

Upload a file via an URL

Hands-on: Data upload from URL

1. Create a new history

   Tip: Creating a new history

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

   If the new-history is missing:

   1. Click on the galaxy-gear icon (History options) on the top of the history panel
   2. Select the option Create New from the menu

2. Copy the following URL

   https://zenodo.org/record/582600/files/mutant_R1.fastq
   

3. Import it in the history

   Tip: Importing via links

   • Copy the link location

   • Open the Galaxy Upload Manager (galaxy-upload on the top-right of the tool panel)

   • Select 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

1. Create a new history

   Tip: Creating a new history

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

   If the new-history is missing:

   1. Click on the galaxy-gear icon (History options) on the top of the history panel
   2. Select the option Create New from the menu

2. Copy the following URL

   https://zenodo.org/record/582600/files/mutant_R1.fastq
   

3. Import it in the history

   Tip: Importing via links

   • Copy the link location

   • Open the Galaxy Upload Manager (galaxy-upload on the top-right of the tool panel)

   • Select 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

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Citing this Tutorial

1. Bérénice Batut, Upload data to Galaxy (Galaxy Training Materials). http://0.0.0.0:4000/training-material/topics/introduction/tutorials/dummy/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{introduction-dummy,
author = "Bérénice Batut",
title = "Upload data to Galaxy (Galaxy Training Materials)",
year = "",
month = "",
day = ""
url = "\url{http://0.0.0.0:4000/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}
}

                   

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/introduction/tutorials/dummy/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

--- {}