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Make sure you have all cables and adapters ready. A list of connectors and a picture how to connect them is available here:
https://github.com/qgc/hardware/wiki/Connectors-and-Peripherals
Follow the instructions on http://wiki.openpilot.org/display/Doc/Firmware+Development+on+Linux but instead of the original repository, checkout the PX2 repository. You don't have to follow the Eclipse import instructions on the OpenPilot Wiki, instead follow the instructions below.
mkdir -p ~/src
git clone http://github.com/qgc/openpilot.git
Import the main folder in to eclipse as existing project (in this case the main folder would be ~/src/openpilot) - you should have all the debug and run targets already in eclipse after the export. The only thing that remains to be done is to right click on the openpilot-flight project and select "Build Configurations -> Set Active -> PX2FMU".
If you prefer to work without Eclipse or you need to unbrick the board, these instructions will give you the minimum set needed to flash the board via JTAG:
https://github.com/qgc/hardware/wiki/PX2-Bringup-and-Unbricking-Notes