Galaxy is an open, web-based platform for performing accessible, reproducible, and transparent biomedical research. Complete computational analyses can be built, saved, rerun, modified and shared. Galaxy is available as a free public web server; as open-source software that can be installed and customized to address specific needs; as a virtual machine that can be installed on the cloud; and on many specialized public web servers at user sites.
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There are many approaches to learning how to use Galaxy. The most popular is probably to just dive in and try it. Galaxy is simple enough to use that you can do many analysis just by exploring the interface. However, you may miss much of the power this way.
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.
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 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 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.
- 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.