I have searched the forum for this issue but didn't find the answer.
I can upload sketches using the arduino IDE from the programming port. I can also upload programs I write in Atmel Studio 6 directly to the SAM3X via the native port using BOSSA with the following command:
bossac -p COM5 -i -e -w -v -b D:\file.bin -R
This all works fine, however, I would like to upload code to the SAM3X using the "programming port" from a command line (not using the arduino IDE).
Does anyone know a good way to do this, or how this can be done? Any assistance or insight will be much appreciated.