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