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Introduction to Galaxy

Contributors

AvatarAndrea Bagnacani AvatarBérénice Batut AvatarSaskia Hiltemann AvatarAnne Pajon AvatarNicola Soranzo AvatarHelena Rasche AvatarChristopher Barnett AvatarMichele Maroni AvatarAnne Fouilloux AvatarNadia Goué AvatarOlha Nahorna AvatarDave Clements
last_modification Last modification: Oct 25, 2021

What is Galaxy?


Galaxy

Data Intensive analysis for everyone

Galaxy resources

Speaker Notes


Core values

Speaker Notes

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

Speaker Notes

Galaxy timeline

Galaxy ecosystem

Galaxy ecosystem

User Interface

Speaker Notes

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

Tools

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[

Speaker Notes

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]


History

Speaker Notes


Multiple histories

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

Speaker Notes


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]

Speaker Notes


Loading data

Speaker Notes

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


Datatypes

Speaker Notes


Reference datasets

Example: reference Genome

.pull-left[

.pull-right[ Genome Builds ]

Speaker Notes


Workflows

Speaker Notes

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

Speaker Notes

Biologist:

Bioinf / dev:


Why would you want to create workflows?

Speaker Notes

Potential information overload for newbies


Visualizations

.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


Community

Speaker Notes


Thank you!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors! Galaxy Training Network This material is licensed under the Creative Commons Attribution 4.0 International License.