Running Command Line in Java

Runtime rt = Runtime.getRuntime();
Process pr = rt.exec("java -jar map.jar time.rel test.txt debug");

http://docs.oracle.com/javase/7/docs/api/java/lang/Runtime.html

You can also watch the output like this:

final Process p = Runtime.getRuntime().exec("java -jar map.jar time.rel test.txt debug");

new Thread(new Runnable() {
    public void run() {
        BufferedReader input = new BufferedReader(new InputStreamReader(p.getInputStream()));
        String line = null;

        try {
            while ((line = input.readLine()) != null)
                System.out.println(line);
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}).start();

p.waitFor();

And don't forget, if you are running a windows command, you need to put cmd /c in front of your command.

EDIT: And for bonus points, you can also use ProcessBuilder to pass input to a program:

String[] command = new String[] {
        "choice",
        "/C",
        "YN",
        "/M",
        "\"Press Y if you're cool\""
};
String inputLine = "Y";

ProcessBuilder pb = new ProcessBuilder(command);
pb.redirectErrorStream(true);
Process p = pb.start();
BufferedReader reader = new BufferedReader(new InputStreamReader(p.getInputStream()));
BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(p.getOutputStream()));

writer.write(inputLine);
writer.newLine();
writer.close();

String line;

while ((line = reader.readLine()) != null) {
    System.out.println(line);
}

This will run the windows command choice /C YN /M "Press Y if you're cool" and respond with a Y. So, the output will be:

Press Y if you're cool [Y,N]?Y

To avoid the called process to be blocked if it outputs a lot of data on the standard output and/or error, you have to use the solution provided by Craigo. Note also that ProcessBuilder is better than Runtime.getRuntime().exec(). This is for a couple of reasons: it tokenizes better the arguments, and it also takes care of the error standard output (check also here).

ProcessBuilder builder = new ProcessBuilder("cmd", "arg1", ...);
builder.redirectErrorStream(true);
final Process process = builder.start();

// Watch the process
watch(process);

I use a new function "watch" to gather this data in a new thread. This thread will finish in the calling process when the called process ends.

private static void watch(final Process process) {
    new Thread() {
        public void run() {
            BufferedReader input = new BufferedReader(new InputStreamReader(process.getInputStream()));
            String line = null; 
            try {
                while ((line = input.readLine()) != null) {
                    System.out.println(line);
                }
            } catch (IOException e) {
                e.printStackTrace();
            }
        }
    }.start();
}