JTAG UART link with non-PC host

Hello,

We're trying to communicate from our host (Atmel ARM under Linux) to our board running NIOS II via the JTAG UART.

We have a valid JTAG chain which is already used to program some MAX-2 and XCF flash. The chain also goes through the FPGA running NIOS.

So far, NIOS can communicate with a host via JTAG UART only when we use a PC and Altera applications, but not our platform.

Is there some sample code available somewhere and/or documentation to illustrate how a custom host must run to communicate with JTAG UART?

Thanks for any help. Nicolas.