Linux sam-ba 2.9

Does anyone know if the Linux sam-ba supports jtag interfaces (such as the Segger SAM-ICE) or is it limited to USB only for board with software jtag? The reason I ask is because on my AT91SAM9263-EK reference board I am able to flash successfully via USB, but I haven’t been able to get JTAG to work at all. This will become a problem on future boards that don’t have the ability to flash via USB, of which I plan to use. What to do? Am I stuck using Windows to flash these board? TIA.