I have scanned SO and found there is no detailed instructions on how to install letsencrypt.org SSL certificate on glassfish and specifically in this tutorial I will be using glassfish 4.1.2 build 1. After a lot of trial and error, I was able to put together the following guide. So I hope that it is fine to ask and answer my own question.
In this tutorial I shall be using an Ubuntu 16.04 LTS Server with Shell access from my Ubuntu 16.04 LTS desktop.