DE1 SoC and UART

I don't know the DE1-SOC, but other SOC demo boards connect the USB UART to the UART built into the SOC. Therefore you don't need a UART component (JTAG or otherwise) in QSYS like you do with a non-SOC board. Check the demos that come on the system disk for the DE1-SOC. There are probably some that use the UART. Write your code to use the UART in the same way that the demos use it. It probably sets up the UART to be the standard C console I/O. You probably don't need fopen.