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 <cmptrwiz...@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
>
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