Practical Bioinformatics

Week 9, Lecture 17

István Albert

Bioinformatics Consulting CenterPenn State

Galaxy

http://www.usegalaxy.org

Creating your own Galaxy

• download the sourcecode

• edit and customise configuration files

• no programming is required

• although one needs to understand certain conventions and details

• requires Python, and runs on linux and mac

Galaxy source-code

Lots of configurations files written as XML markup

tool_conf.xml

Galaxy is an interface to tools!

Update the configuration file

Create the parameters for the tool

Slowly populating the interface

How does genomeCoverageBed work?

Adding more parameters and a command

The new interface

More customizations

Real Galaxy many tools

Galaxy Feature walktrough

• getting data into galaxy

• data types

• setting data properties

• exploring tools and techniques