[galaxy-dev] Developing Tools With Java

Hello,

I just started working with developing a tool for Galaxy; I have been programming it in Java. However, when it came time to implement my tool into Galaxy, I was unable. When I try to run it normally, it works. However, in Galaxy, when I try to use the JAR file, it produces a java.lang.NoClassDefFoundError and a java.lang.ClassNotFoundException.

As it seems rather meaningless to be setting a classpath in an abstract framework like Galaxy, is there a simple way to run Java JAR files? I tried a "-jar" argument, but I can't put in an argument before the filename. Should I be using the ".class" files instead of the JAR files? Should the format in the XML file be <command interpreter="java"></command>?

Thanks so much, Elie