Actually if the file is called getseq.java, you need to compile it first. (Generally you do this with:

javac getseq.java

although if it uses extra libraries you'll have to add those to the classpath:

javac -classpath foo.jar getseq.jar

Then, assuming that the java binary is in your PATH and the getseq.class file is in /path/to/getseq, you can run:

system "java -classpath /path/to/getseq getseq dir1 dir2"

But this is getting OT for Perlmonks :-)

Chris
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