If you wish to program the Arduino-compatible side of UDOO from your Pc, Mac or Linux computer,

just follow these easy steps to get started.
First of all, check that these requirements are met:

• A working SD Card should be present on UDOO
• J18 jumper should be unplugged. This will allow the communication between your computer and the programming port of the SAM3X
  
• The Micro USB cable should be plugged in the Sam3x port, not the one you would normally use for serial USB connection
  

If all the requirements above are met, you’re ready to start. What we will basically do is configure the standard Arduino-IDE in order to make it communicate to the Sam3x of UDOO, which is the Arduino-compatible micro-controller.

To do so:

• Download and install the Arduino IDE version 1.5 for your specific operating system from the official website (other versions will not work, since UDOO needs Arduino 2 compabile programming software)
• Download the patch for your Operating system here
• Extract the files in the archive and place them in the following paths, overwriting the previous existing files:
  In Windows 32 bit:
  C:\Program Files\Arduino\hardware\tools
  In Win 64 bit:
  C:\Program Files (x86)\Arduino\hardware\tools
  In Linux:
  /hardware/tools/
  In Mac OS X:
  /Contents/Resources/Java/hardware/tools/
• With this patch you are now able to upload your sketch selecting the Arduino Due(Programming Port) from:
  Tools -> Board and the right port from Tools -> Port in the Arduino IDE