This is probably going to sound rather vague and probably won't yield any responses, but I'm going to ask anyway..

For my job (random tech support/software stuff), one of my bosses asked me to build a website that would act as an interface between a .jar file and a user. If you were using this program on your local machine, it would be called in the DOS command prompt (as would all of the commands to it), but I'm supposed to design this interface so that the program can be accessed remotely from our server.

Does anyone have any (even vague) idea how to go about this?
I just need guidance in the right direction and I can (hopefully) figure out the rest from there.