It varies with the distro, but in general, the system wide environmental variables are normally setup in /etc/profile. However, using /etc/bashrc should accomplish the same thing. Not sure exactly what you are trying to do. To run a .jar file in linux, you would usually run:
$ java -jar app.jar
if you have the java /bin directory in PATH. To have a launch icon from the desktop you could create a bash script(s) that could do that. Post back if you need more details.
Last edited by kilgoretrout; 01-30-2007 at 10:44 AM.