Service that runs every minute

You need to exit the main thread to avoid risking a ANR.

Instead add a Handler

Handler mHandler = new Handler();

...

@Override
protected void onHandleIntent(Intent intent) {
    Toast.makeText(this, "onhandleintent", Toast.LENGTH_SHORT).show();
    mHandler.postDelayed( ToastRunnable, 5000);
    //while(true)
    //{

        //one minute is 60*1000
        //try {
        //    Thread.sleep(5 * 1000);
        //    Toast.makeText(getApplicationContext(), "getting app count",          
        //Toast.LENGTH_LONG).show();
        //} catch (InterruptedException e) {
            // TODO Auto-generated catch block
        //    e.printStackTrace();
        //}
    //}
}
final Runnable ToastRunnable = new Runnable(){
    public void run(){
         Toast.makeText(getApplicationContext(), "getting app count",          
               Toast.LENGTH_LONG).show();
         mHandler.postDelayed( ToastRunnable, 5000);
    }
}

Do it like this

    private void ping() {
    try {
        //Your code here or call a method
    } catch (Exception e) {
        Log.e("Error", "In onStartCommand");
        e.printStackTrace();
    }
      scheduleNext();
    }

    private void scheduleNext() {
      mHandler.postDelayed(new Runnable() {
        public void run() { ping(); }
      }, 60000);
    }

    public int onStartCommand(Intent intent, int x, int y) {
      mHandler = new android.os.Handler();
      ping();
      return START_STICKY;
    }

This will send an intent to your service every minute without using any processor time in your activity in between

  Intent myIntent = new Intent(context, MyServiceReceiver.class);
  PendingIntent pendingIntent = PendingIntent.getBroadcast(context,  0, myIntent, 0);

  AlarmManager alarmManager = (AlarmManager)context.getSystemService(Context.ALARM_SERVICE);
  Calendar calendar = Calendar.getInstance();
  calendar.setTimeInMillis(System.currentTimeMillis());
  calendar.add(Calendar.SECOND, 60); // first time
  long frequency= 60 * 1000; // in ms 
  alarmManager.setRepeating(AlarmManager.RTC_WAKEUP, calendar.getTimeInMillis(), frequency, pendingIntent);           

Adjust MyServiceReceiver.class to match your target service or activity. The documentation provides more details to fine-tune your calls like whether you want exact timing, execution at a specific time of the day ...