really isnt much different just copy your win32 q3 folder over to your linux box and put the cnq3 binaries in and run it with the same commands you ran the win32 one with. for a basic bash script you could do something like this:

#!/bin/bash
cd /where/your/q3/is/at
./cnq3 -blah -blah

i dont know what commands you need for it but im guessing it something like -set dedicated 1 but really its going to be the same as in win32