I use XFCE but this solution should work for any desktop environment on Debian or Ubuntu:
XKBOPTIONS definition in
This affects all users on the system.
This won't affect your current session (you have to restart X11),
so you can run this command line to change things until then:
$ setxkbmap -option ctrl:nocaps
To affect only your user, have the above command run as a part of your session: Open your XFCE Settings (run
xfce4-settings-manager) and click on Session and Startup, go to the Application Autostart tab, and Add that command.