> For the complete documentation index, see [llms.txt](https://igb.mit.edu/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/galaxy/intro-to-galaxy.md).

# Intro to Galaxy

### Background

Galaxy is a framework for integrating computational bioinformatics tools. It provides a common interface that wraps diverse tools, as well as an environment for interactive analysis that transparently tracks the details of analysis steps, a workflow system for convenient reuse, data management, sharing, publishing, and more.

The web-based Galaxy site is freely available to the public. User registration at the site is optional, but can be beneficial to increase its efficiency for the user. The registration is free and allows the user to create custom workflows and save analysis results.

Open [this link](http://main.g2.bx.psu.edu/) in a new window or type <http://main.g2.bx.psu.edu/> in your url bar. In the main page of Galaxy, you will find some introductory material, including useful screencasts that show how to use the various tools to perform many types of analyses, such as text manipulation, format conversion, NGS quality control, NGS Mapping, interval data manipulations, relational database operations, and many more.

### General Information

* There are three panes in the Galaxy desktop:
  * Tool pane (left).
  * Current Analysis pane (centre).
  * Job/History pane (right).

<figure><img src="/files/mLzZtbGn7AvHPZVG3FBI" alt=""><figcaption></figcaption></figure>

* To analyze the data in Galaxy, you perform an ordered sequence of tasks, each consisting in applying a specific tool (chosen from the left pane) to a specific set of files (chosen in the central pane or among the results from previous steps as reported in the History pane).
* The History pane shows the sequence of steps/tasks you are running. In particular, the color of the frame associated with a particular job has the following meaning:
  * gray : the job is in the queue.
  * yellow: the job is running.
  * green: the job is completed.
  * red: the job produced an error.


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