GOBBLER:
package org.jamescarr.payfuse.fit;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;


public class StreamGobbler extends Thread {

	private InputStream is;

	private String type;

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

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

COMMANDLINE RUNNER:
package org.jamescarr.payfuse.fit;

import java.io.IOException;




public class PayFuseTest {


	public static void main(String[] args) {
		PayFuseTest pf = new PayFuseTest();
		try {
			pf.testInput();
		} catch (IOException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		} catch (InterruptedException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}
	}

	public void testInput() throws IOException, InterruptedException {

		String[] command = new String[3];

		command[0] = "/bin/ls";
		command[1] = "-al";
		command[2] = "/home/jamescarr/";
		Process proc = Runtime.getRuntime().exec(command );

		// any errors?
		StreamGobbler errorGobbler = new StreamGobbler(proc.getErrorStream(),
				"ERROR");

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


		errorGobbler.start();
		outputGobbler.start();

		int exitCode = proc.waitFor();
		System.out.println("exit code: " + exitCode);

	}
}