Hi Frederick,
I'm not an expert but maybe you could consider to write a python wrapper to call your Java application.

---
Marco


On 7 May 2011 08:08, Frederick van Staden <cmptrwizard@gmail.com> wrote:
Hello!

Im looking for a way to run jar files(or class files) as a tool.
Im not sure how to setup the galaxy instance to do this.
For some reason i am running into a classpath issue.

 Anyone that could guide me in the right direction?


Regards
Frederick

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/