Requirements

Before diving into this slide deck, we recommend you to have a look at:

• Introduction to Galaxy Analyses
  • Galaxy Basics for genomics: tutorial hands-on

question Questions

• How do I get my data into Galaxy?

• How do I get public data into Galaxy?

Getting 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

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

Source: Galaxy Community Hub

1. The Get Data toolbox section

• Click on the Get Data toolbox in the toolbox (the left panel)

• Expands to show data sources

  • E.g. UCSC, NCBI, Uniprot, ..
  • 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

2. Import from Shared Data Library

You can select the files you want and send to History as datasets or collection

3. Upload from your computer

Choose files

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)

• Can be set for all files at once:

• Or per file:

Start upload process:

• Once everything is ready, click the Start button

All the items will appear in your history

and are ready to use when green.

Directly enter text

• Sometimes it's useful to file content directly.
  • only works if your dataset is tiny
  • choose Paste/Fetch data

Enter the data by typing (or pasting) it in the input box:

You can also set the datatype and build. Click Start, and then Close, and the new item shows up as Pasted Entry in your history.

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.

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
  • See https://galaxyproject.org/ftp-upload/

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. usegalaxy.org, ftp.usegalaxy.eu)
  • your full username (usually an email address) and password

Successfully connected

Right click on the files and upload them.

FTP Transfer in progress...

... and transfer complete.

Where did my files go?

• File Upload menu -> Choose FTP files

• Select files to import into your history
• Click Start

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

• Collection is now imported in your history
• Click on it to expand it and view all files in collection

Import using Rule Based uploader

• When you want to import many files from URLs or Accession IDs directly into collection(s)
• Supports advanced "rules" for creating collections from sample sheets
• Click Rule-based tab at top of file upload window

Import using Rule Based uploader

Learn how to use it in the dedicated Rule Based Uploader tutorial

Thank You!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors!

Author(s)	Anne Pajon Dave Clements Maria Doyle Saskia Hiltemann
Reviewers

Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.