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();

You need Runtime.getRuntime().exec(...). See a very extensive example (don't forget to read the first three pages).

Keep in mind that Runtime.exec is not a shell; if you wish to execute a shell script your command line would look like

/bin/bash scriptname

That is, the shell binary you need is fully qualified (although I suspect that /bin is always in the path). You can not assume that if

myshell> foo.sh

runs,

Runtime.getRuntime.exec("foo.sh");

also runs as you are already in a running shell in the first example, but not in the Runtime.exec.

A tested example (Works on My Linux Machine(TM)), mosly cut-and-past from the previously mentioned article:

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
public class ShellScriptExecutor {

    static class StreamGobbler extends Thread {
        InputStream is;

        String type;

        StreamGobbler(InputStream is, String type) {
            this.is = is;
            this.type = type;
        }

        public void run() {
            try {
                InputStreamReader isr = new InputStreamReader(is);
                BufferedReader br = new BufferedReader(isr);
                String line = null;
                while ((line = br.readLine()) != null)
                    System.out.println(type + ">" + line);
            } catch (IOException ioe) {
                ioe.printStackTrace();
            }
        }
    }


    public static void main(String[] args) {
        if (args.length < 1) {
            System.out.println("USAGE: java ShellScriptExecutor script");
            System.exit(1);
        }

        try {
            String osName = System.getProperty("os.name");
            String[] cmd = new String[2];
            cmd[0] = "/bin/sh"; // should exist on all POSIX systems
            cmd[1] = args[0];

            Runtime rt = Runtime.getRuntime();
            System.out.println("Execing " + cmd[0] + " " + cmd[1] );
            Process proc = rt.exec(cmd);
            // any error message?
            StreamGobbler errorGobbler = new StreamGobbler(proc
                    .getErrorStream(), "ERROR");

            // any output?
            StreamGobbler outputGobbler = new StreamGobbler(proc
                    .getInputStream(), "OUTPUT");

            // kick them off
            errorGobbler.start();
            outputGobbler.start();

            // any error???
            int exitVal = proc.waitFor();
            System.out.println("ExitValue: " + exitVal);
        } catch (Throwable t) {
            t.printStackTrace();
        }
    }
}

create a file named "sync" in /usr/bin containing the following:

java -jar {PATH TO JARFILE} $1 $2

Replace {PATH TO JARFILE} with the path to the jarfile

Make the file executable by typing chmod +x sync while in /usr/bin