njgit edited this page Oct 27, 2011 · 49 revisions

Welcome to the App-Galaxy-Devel-Tool wiki!

What is galaxp?

Installing the App-Galaxy-Devel-Tool distribution from cpan provides the galaxp command line application that aids the development of Perl tools on the galaxy bioinformatics platform in the cloud.


An example for integrating a Perl tool script with galaxy is given on They indicate 5 steps to integrating a custom galaxy tool on galaxy.

  1. Write and test your tool outside GALAXY
  2. Put tool into GALAXY's {{{tools}}} directory
  3. Create Tool Definition File
  4. Make GALAXY aware of the new tool
  5. Start it up

This command line app was developed to make aspects of developing galaxy tools on the galaxy community AWS cloud instances easier.


First save the access details for your AWS instance

galaxp save --host --key_file /path/to/key.pem

Then to initiate the above step 1 (Write and test your tool outside GALAXY).

galaxp new mytool ( Perl galaxy tool named "mytool")

By default this creates a Perl distribution called GalaxyX-Tool-mytool configured and ready for writing and testing a galaxy Perl tool. More about writing and testing is here.

(Note the prefix GalaxyX-Tool can be changed or omitted )

After this, steps 2 - 5. are achieved with the push command

galaxp push GalaxyX-Tool-mytool

Your galaxy tool is now deployed and available to view on your remote master galaxy instance! This includes the installation of any prerequisite Perl modules.