It is designed to help two communities rarely talking to each other: 1. Experimental biologists : "I really have no time to program but I want to do whole-genome analyses to find targets for experimental validation". 2. Computational biologists : "I develop algorithms but have no time to develop interfaces". So, decide which category you belong to and follow me... Galaxy = interactive and reproducible genomics
Galaxy homepage Tools frame Main frame Operation history frame
Galaxy installation svn co http://www.bx.psu.edu/svn/universe/galaxy/trunk galaxy_dist Just few lines of commands to install galaxy on your Mac cd galaxy_dist cp universe_wsgi.ini.sample universe_wsgi.ini cp tool_conf.xml.sample tool_conf.xml cp datatype_converters_conf.xml.sample datatype_converters_conf.xml sh run.sh If all the required libraries are correctly installed (sometimes unfortunately that is not…)
So let’s start!!! You can upload all these file format, the platform manage, more or less, whatever you want!!! … or simply copy&paste in the box.
Many and many tools are already available, but… … customized is better!!! Suppose you has written a simple PERL script for analyzing some kind of data >perl toolExample.pl $input $option1 $option2 $output - Put tool into GALAXY's /tools directory creating your personal subdirectory /tools/myTools: - Create Tool Definition File (xml) - Make GALAXY aware of the new tool - Start it up!!! Just 4 steps:
Create Tool Definition File (xml) <tool id=”chip-chip_analysis" name=”PeakPicker"> <description>Finding Peaks in a GFF Nimblegen File</description> <command interpreter="perl">toolExample.pl $input $option1 $option2 $output</command> <inputs> <param format=”gff" name="input" type="data" label="Source file"/> <param name=”option1" type=”integer” label=”Option 1" /> <param name=”option2" type="data_column" data_ref="input" numerical="True" label=”Option 2" /> </inputs> <outputs> <data format=”bed" name="output" /> </outputs> </tool> Save it as : toolExample.xml in your tools subdirectory To let GALAXY know the execution details of our new tool we need to write a tool configuration file
Make GALAXY aware of the new tool GALAXY knows about installed tools (and also what to display on the left panel) from the tool_conf.xml tool-registry file. <section name="MyTools" id="mTools"> <tool file="myTools/toolExample.xml" /> </section> Just adding: