I couldn't find a good example of this, so here's how you use a PumpStreamHandler from commons-exec from the apache
public static void main(String a[]) throws Exception
{
ByteArrayOutputStream stdout = new ByteArrayOutputStream();
PumpStreamHandler psh = new PumpStreamHandler(stdout);
CommandLine cl = CommandLine.parse("ls -al");
DefaultExecutor exec = new DefaultExecutor();
exec.setStreamHandler(psh);
exec.execute(cl);
System.out.println(stdout.toString());
}