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:

Topic Overview slides

instances Available on these Galaxies

docker_image Docker image

Last modification: Oct 18, 2022

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

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

Introduction

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

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

Select Paste/Fetch Data

Paste the link 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

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

Select Paste/Fetch Data

Paste the link 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

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Citing this Tutorial

Bérénice Batut, 2022 Upload data to Galaxy (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/introduction/tutorials/dummy/tutorial.html Online; accessed TODAY
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 = "2022",
month = "10",
day = "18"
url = "\url{https://training.galaxyproject.org/training-material/topics/introduction/tutorials/dummy/tutorial.html}",
note = "[Online; accessed TODAY]"
}
@article{Batut_2018,
    doi = {10.1016/j.cels.2018.05.012},
    url = {https://doi.org/10.1016%2Fj.cels.2018.05.012},
    year = 2018,
    month = {jun},
    publisher = {Elsevier {BV}},
    volume = {6},
    number = {6},
    pages = {752--758.e1},
    author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{\i}}rez and Devon Ryan and Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Björn Grüning},
    title = {Community-Driven Data Analysis Training for Biology},
    journal = {Cell Systems}
}
                   

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