Programming due with pi

Hi, I've been searching everywhere and I can't find an answer to this. I am planning on designing a custom board with the sam3x processor and I'm attempting to program it with the raspberry pi. I can program the due with the bossac gui in ubuntu no problems via the usb ports, but I eventually wanted to ditch the 16u2 interface and go directly into the first uart (Tx0 & Rx0). I pulled out the datasheet on the sam3x and my understanding is that if I press the erase button, the sam3x should boot into samba which looks for programming on the native port or uart, is that right? Bossac doesn't even recognize the due this way.

Any questions or if I've left any important info out please ask and any ideas would be helpful. Thanks.


this does not answer your question, but is related (I have not tested yet).
There is an Ardiuno IDE available for the Raspberry Pi, but version 1.0.5 is very outdated.
In Kolban's book there is this Github link allowing you to install latest Arduino IDEs on Raspberry (including Zero, will try to do that):

With this you can use any Pi to run Arduino IDE and program any Arduino (including the Pi "as Arduino" via the RasPiArduino project on Github).


Thanks for the reply, but like I said I have no problem programming the due with the pi using the bossac command line interface via usb. My problem here is a hardware issue. I want to see if I can ditch the 16u2 programming interface and program the due directly with the pi via the uart. I did find somewhere, someone said that it couldn't be done as jessie isn't a real time operating system. I just want to know if someone has tried and come up with the conclusion that it can't be done because he didn't back anything up, I just want to understand exactly why it can't be done because from what I know/see, it can, but I can't figure it out haha.