Upload data to Galaxy

Authors: orcid logoAvatarBérénice 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:
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
  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

    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

    • 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
  1. Create 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

    • 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

  1. 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
  2. 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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