There are many approaches to learning how to use Galaxy. The most popular is probably to just dive in and use it. Galaxy is simple enough to use that you can do many analyses just by exploring the interface. However, you may miss much of the power this way.

Galaxy 101

Walking through the Galaxy 101 exercise will show you the ins and outs of using Galaxy. This includes loading data (from UCSC in this example), using genome builds, the tool interface, filtering, sorting, and combining datasets, generating statistics, and Galaxy's History, Workflow and sharing support.

Galaxy 101 is available in several formats. You can start with either the Galaxy Page or the screencast.

Screencasts

There are a plethora of Screencasts available that demonstrate many aspects of Galaxy from basic features to full-blown complex analysis. See the Screencasts page for more.

Shared Pages, Histories & Workflows

Another way to learn Galaxy is by learning from what others have done. Galaxy supports the sharing and publishing of several Galaxy Objects within Galaxy:

• Pages - Pages are documentation within that Galaxy that explain the steps and reasoning in a particular history or workflow. They provide additional context and can describe why particular choices were made. The list of published pages is a great place to start.

• Histories - Histories are analyses in Galaxy that show all input, intermediate, and final datasets, as well as every step in the process and the settings used with each. Histories can be imported into your session and rerun as is or modified. See the Managing Histories screencast.

• Workflows - Workflows specify the steps in a process but not the datasets. Workflows are analyses that are meant to be run, each time with different user-provided datasets.

• Data Libraries - Datasets that are accessible from within Galaxy or for download.

Other Tutorials

In addition to Screencasts and Shared Pages, Histories & Workflows. There are now several Galaxy-centric tutorials and "how to" papers that have been created by the community:

Datasets

Galaxy for many users is all about Datasets, the inputs and outputs of analysis jobs. Learn how to load, label, format/reformat, QC, manipulate, visualize, detect problems in, save, share, hide, delete, perform simple-to-complex manipulations, generate standard and custom statistics, and track the methods that create datasets.

Learning the basics of how to manage datasets helps focus analysis on the scientific aspects of a project, minimizing problems and troubleshooting. Simply put, save time and verify format first! Quick to do right in the existing history, no programming required.

• Using Custom Genomes - Format, loading, troubleshooting, and tools.

• Managing Datasets - Attributes, Copy, Clone, Delete and more.

• Datatypes - Specifications for the datatypes used and produced by Galaxy's tools.

• Main and Test Quotas - User account allocations for data and jobs.

• Data management: accounting and disk quotas - Implementation details.

• Learn/DataSources - Sources, Credits, and Methods for standard native data

• Admin/Datatypes & Admin/Data Integration - Instructions about adding new datasets (genomes) and datatypes to a local Galaxy instance

Tools

Extensive help on how to use a particular tool in Galaxy is often included on the tool page itself, inside Galaxy. To see this help, click on a tool in the left tool panel, and then scroll to the bottom of the center panel. Help includes parameter explanations, links to tool developers' help pages, and examples.

The long term plan is also to have a wiki page for each widely installed tool in Galaxy. These pages will hold supplementary information about both using the tools and setting them up. However, we haven't set that up yet.

In the meantime, for some tools there is also additional information available on this wiki:

• Interval Operations - Help on tools that operate on genomic intervals.

• UCSC Galaxy Integration

• Share - How to share your Galaxy objects with others.

• FTP Upload - Having problems loading larger (>2MB) files into Main? Watch FTP Upload

• Uploading and Analyzing Genotype Data in Plink Format

Visualization

Galaxy incorporates a track browser. This can be used to visualize genomic data within Galaxy in a tightly integrated way. The browser also currently supports (and aims to support maximally) visual analytics, where visualization is used iteratively to provide feedback on analysis. See Visualization for more.

User Accounts

Galaxy user accounts are simple to create (email, password, user name and go!). An account is not required to access the Galaxy public Main or Test instances, but if used, the data quota is increased and full functionality across sessions opens up, such as naming, saving, sharing, and publishing Galaxy objects (Histories, Workflows, Datasets, Pages).

• User Accounts

• OpenID Login

• Security Features

Other

• Big Picture/Choices - The Galaxy Main server is not your only choice for using Galaxy.

• Interactive Poster

• Admin - How to administer your own Galaxy instance