I use XFCE but this solution should work for any desktop environment on Debian or Ubuntu:
Replace the XKBOPTIONS definition in /etc/default/keyboard with
XKBOPTIONS="ctrl:swapcaps"
This affects all users on the system. Replace with ctrl:nocaps if you want no keys to act as caps lock.
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:swapcaps
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.