Creating pulses through parallel port

What also helps if you give an overview of your complete project, rather than just a little bit at a time.
If you just want to run a single stepper Linuxcnc may be overkill, operating the parallel port via a simple C program may be easier, but that will mean obtaining permissions from the kernel to do these, and running in user space may not give consistent timings for the stepper.
The other option would be to have a hardware base approach and use python or what ever to control when the stepper runs & stops.
Even a simple Arduino sketch controlled by via a serial connection would be easy. Depending on the library used you could have control over decel & accel.