View markdown source on GitHub

Getting data into Galaxy



last_modification Last modification: Dec 6, 2023

Getting data into Galaxy

Speaker Notes

-> Pressing P will toggle presenter mode.

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

Speaker Notes

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

flowchart for getting data into galaxy. SRA datasets should use the upload tool, if you have many or big datasets use FTP, if they're from the web use the URL upload.

.footnote[Source: Galaxy Community Hub]

1. The Get Data toolbox section

Click on Get Data to expand it

.pull-right[.image-75[A typical list of data sources]]

Speaker Notes

This shows the list of data sources that were available on in mid 2017.

Two large data sources you can access through Galaxy are UCSC and SRA

.pull-right[Screenshot of toolbox with ucsc entered in search] .pull-left[galaxy toolbox with sra entered in search box.]

2. Import from Shared Data Library


.pull-right[galaxy top menu dropdown shared data, showing Data Libraries]

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

.image-75[data library screenshot with a number of datasets selected and export to history menu open]

3. Upload from your computer

.image-50[click on upload button]

Upload file form

Speaker Notes

This is probably the most commonly used tool for bringing data into Galaxy, and it is installed on almost every Galaxy server.

Choose files

Options for importing files from your laptop

Speaker Notes

Set Metadata

upload dialog from galaxy with a number of files queued.

Speaker Notes

Set datatype for all imported datasets

Manually set datatype for one dataset

Speaker Notes

Start upload process:

Ready to upload files. Click on start

Speaker Notes

You can then close the form

Ready to upload files. Click on start

Speaker Notes

All the items will appear in your history

Files are loaded into your current history.

and are ready to use when green.

Directly enter text

Select Paste/Fetch data

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

Select Paste/Fetch data

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

Select Paste/Fetch data

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

Select Paste/Fetch data

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

Import using FTP

Make sure you have an FTP client installed


Establish FTP connection to your Galaxy server

FTP Connection Params

Successfully connect

Successfully connected

Navigate to the files you want to transfer

Right click on the files and upload them.

FTP transfer in progress

FTP Transfer in progress…

FTP transfer complete

… and transfer complete.

Where did my files go?

choose FTP files

choose FTP files

Speaker Notes

As you can see, this dialog gives connection settings too

Import directly into Collection

Direct collection Start

Direct collection Build

Direct collection Name

Direct collection History

Import using Rule Based uploader

Rule Uploader

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! Galaxy Training Network Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.