Gssoftware

Download QGroundControl

mkdir -p ~/Projects
git clone git://github.com/pixhawk/qgroundcontrol.git

Install Debian Dependencies

cd ~/Projects/qgroundcontrol
./autobuild.sh (select 3)
qmake
make

Start QGroundControl

cd ~/Projects/qgroundcontrol ./release/qgroundcontrol

Connect Autopilot

Click connect link. Settings:

1. Serial Port: of FTDI cable (e.g. /dev/ttyUSB)
2. Select emit heartbeat option.
3. Baud Rate: 115200