I have downloaded the newest version of Arduino (to use with my Arduino Due) from here: http://downloads.arduino.cc/arduino-1.5.6-r2-linux64.tgz.
At the moment I have extracted it into /home/$USER and am running it by going into arduino-1.5.6-r2 and running the executable directly.
How can I have it so it is installed as it would be if I had downloaded it using apt-get install arduino?