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Introduction to Galaxy


last_modification Published: Sep 30, 2016
last_modification Last Updated: May 3, 2024

What is Galaxy?


Data Intensive analysis for everyone

Galaxy resources

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Core values

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accessible reproducible transparent research means sharing everything.

The Galaxy framework aims to make as simple as possible for researchers to:

Pages: interactive, web-based documents that describe a complete analysis.

Galaxy growth

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Galaxy timeline

Galaxy ecosystem

Galaxy ecosystem

User Interface

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So now that we know what Galaxy and the Galaxy Project are all about, let’s look at the Galaxy interface.

Main Galaxy interface

Galaxy user interface

Home page divided into 3 panels

Top menu

Top menu

Link Usage
galaxy-home (or Analyze Data) go back to the homepage
Workflow access existing workflows or create new one using the editable diagrammatic pipeline
Visualize create new visualisations and launch Interactive Environments
Shared Data access data libraries, histories, workflows, visualizations and pages shared with you
Help links to Galaxy Help Forum (Q&A), Galaxy Community Hub (Wiki), and Interactive Tours
User your preferences and saved histories, datasets, pages and visualizations


Tool interface

Tool interface

.pull-left[.image-50[Screenshot of the tool interface for the Sort tool showing some inputs and an execute button.]] .pull-right[

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The tool form is generated from a simple XML file describing:

Tools can be viewed as tiny LEGO pieces: each one solves a specific problem, and they can be combined together to build complex analysis pipelines.

Tool Shed

.image-50[Screenshot of the toolshed homepage]


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Multiple histories

.image-75[Screenshot of galaxy showing multiple histories next to each other in the multi-history view]

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History options menu

.pull-left[ History behavior is controlled by the History options (gear icon) History menu ] .pull-right[ .image-75[History options gear button]

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Loading data

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So now you know about the tools to manipulate data and the history where you can see your data, your inputs and outputs. Let’s discuss how to get data into Galaxy

Importing data

See Getting data into Galaxy


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Reference datasets

Example: reference Genome


.pull-right[ Genome Builds ]

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Now that you’ve got data into Galaxy, you know you can use tools to manipulate this data, and histories to keep track of what you’ve done. You’re only missing one key part: workflows. These help you easily reproduce the exact analysis that you ran.

Workflow Editor

Workflow interface

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Bioinf / dev:

Why would you want to create workflows?

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Potential information overload for newbies


.image-75[Examples of 6 different visualisations in galaxy features an MSA, a couple graphs, RNA structure, and 3d visualisations of proteins]

Sharing data

See Sharing your History in Galaxy


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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.