You should really look at Process Builder. It is really built for this kind of thing.
ProcessBuilder pb = new ProcessBuilder("myshellScript.sh", "myArg1", "myArg2");
Map<String, String> env = pb.environment();
env.put("VAR1", "myValue");
env.remove("OTHERVAR");
env.put("VAR2", env.get("VAR1") + "suffix");
pb.directory(new File("myDir"));
Process p = pb.start();
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