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introduction to galaxy

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Nuova piattaforma bioinformatica …

Nuova piattaforma bioinformatica


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  • 1. Galaxy http://g2.trac.bx.psu.edu/ Matteo Cesaroni
  • 2. 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
  • 3. Galaxy homepage
  • 4. Galaxy homepage Tools frame Main frame Operation history frame
  • 5. 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…)
  • 6. 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.
  • 7. 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:
  • 8. Create Tool Definition File (xml) <tool id=”chip-chip_analysis&quot; name=”PeakPicker&quot;> <description>Finding Peaks in a GFF Nimblegen File</description> <command interpreter=&quot;perl&quot;>toolExample.pl $input $option1 $option2 $output</command> <inputs> <param format=”gff&quot; name=&quot;input&quot; type=&quot;data&quot; label=&quot;Source file&quot;/> <param name=”option1&quot; type=”integer” label=”Option 1&quot; /> <param name=”option2&quot; type=&quot;data_column&quot; data_ref=&quot;input&quot; numerical=&quot;True&quot; label=”Option 2&quot; /> </inputs> <outputs> <data format=”bed&quot; name=&quot;output&quot; /> </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
  • 9. 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=&quot;MyTools&quot; id=&quot;mTools&quot;> <tool file=&quot;myTools/toolExample.xml&quot; /> </section> Just adding:
  • 10. ..and now start it up!!! Use your tools!!!