How to tell my computer to run a program on fpga

You will need to add a PCIe core to your FPGA. Then map your Slave IP onto the address map of the End Point PCIe. Then write the driver for the PC to talk to your slave.

Btw, I dont think PCIe is a free IP core from Altera, you need to buy it as an add-on to your licence, as is ethernet. For a simple interface there is RS232 that you can drive through a serial port on your PC (or via a cheap usb-> serial cable).