Well,
i ask this question, because i'm confused.
basicly under linux, there a two type of "programs".
1) a normal application: a normal application doesn't access the hardware directly or uses kernel functions. it will use a driver -> system calls (program runs in user-space).
if try to access kernel functions from an application i don't know. you might have to trick a lot.
you can try to register the interrupt manually without linux (study the altera hal sources).
2) a kernel module ("driver") gets direct access to the hardware and can use kernel function, so i was thinking you are going to write a driver...