Training Course in Galaxy for Metagenomic Analysis on Targeted and Whole Genome Sequencing Data

Getting data into Galaxy

How do I get my data into Galaxy? How do I get public data into Galaxy?

Many ways to get data into your workspace

  1. Import using Get Data sources e.g. UCSC, SRA
  2. Import from a Galaxy Data Library
  3. Import using Upload File
    • Import from your computer
    • Directly enter text
    • Import from a URL
    • Import using FTP
    • Import directly into Collection
    • Import using Rule Builder

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Best method depends on where the data is, and how big it is

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The Get Data toolbox section

  • Click on the Get Data toolbox in the toolbox (the left panel)
  • Expands to show data sources
    • The specific data sources available on your Galaxy instance are determine by the server’s administrator
  • All of these data sources can bring datasets (files) into your Galaxy workspace (history)
  • Two large data sources you can access through Galaxy are UCSC and SRA

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Import from Shared Data Library

  • Top menu bar -> Shared Data -> Data Libraries
  • Configured by a Galaxy Administator
  • Can be imported directly into your history

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Upload from your computer

  • At the top of the Tools panel (on the left), click Upload This brings up a box:

  • The Upload File data source can import data:

    • from your computer
    • by directly entering text
    • using a URL
    • and via FTP

Choose files

  • Drag and drop is supported
  • as is the standard file selection using your browser.

Set Metadata

  • Datatype (e.g. FastQ, VCF, BAM, tabular, ..)
    • Galaxy will autodetect by default (sometimes guesses wrong)
  • Genome Build (e.g. hg19, mm9, ..)
    • must be set manually (can be done later as well)
  • Click Start, and then Close, and the new items show up in your history with the URL as their name.

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Import using URL

The data might already be available on a web server somewhere. To avoid downloading data to your computer and uploading to Galaxy in two steps, you can instruct Galaxy to directly fetch the data from a given URL.

  • Select Paste/Fetch data

  • Enter the URLs (one per line) into the input box:

  • Click Start, and then Close, and the new items show up in your history with the URL as their name.

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Import using FTP

  • Why use FTP?
    • Older Galaxies did not support uploading files larger than 2GB in size
    • Many people are very comfortable using FTP to upload large datasets and you can sometimes resume interrupted uploads.
  • How to use FTP
    • The Galaxy server’s administrator must have enabled FTP on the server
    • You will need to create an account on that Galaxy Server
    • You will need to install FTP software, or to run FTP from the shell

Make sure you have an FTP client installed

  • FileZilla is a free FTP client that is available on Windows, MacOS, and Linux
  • There are many other options
  • If you don’t already have an FTP client, download and install FileZilla.

Establish FTP connection to your Galaxy server

  • Provide
    • the instance’s FTP server name (e.g. izs3.crs4.it, usegalaxy.org, ftp.usegalaxy.eu)
    • your full username (usually an email address) and password

  • Right click on the files and upload them.

Where did my files go?

  • File Upload menu -> Choose FTP files

  • Select files to import into your history
  • Click Start

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Import directly into Collection

  • Select Collection tab at top of upload menu
  • Add files as before (upload from computer, paste/fetch, FTP)

  • Choose collection type (at bottom)
  • Set metadata (file type, genome build)
  • Click Build

  • Name your collection
  • Click Create button

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