Everytime I need to launch a native program from Java I always end up with this old guide. It covers all that is needed to execute a native application from Java.
http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html
If you are fine with including 3rd party libraries here is a guide using the Executor from the apache commons project:
http://java.dzone.com/articles/executing-command-line
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