In a GWT application without GAE you can use Runtime.getRuntime().exec("some command");
If you want to read out the result of the command, you can use:
Process p = Runtime.getRuntime().exec("A command");
BufferedReader in = new BufferedReader(new InputStreamReader(p.getErrorStream()));
StringBuilder builder = new StringBuilder();
String line = null;
while ((line = in.readLine()) != null) {
builder.append(line + "\n");
}
String result = builder.toString();
If the command above should not work, i guess you have to remove GAE from your project to run a bash script.