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