This guide will show you how to program an Arduino connected to your Raspberry PI from the Arduino IDE on your local computer. Linux and OS X for now

On your Raspberry PI

First install avrdude

apt-get install avrdude

Install avrdude-rpi using the installation tips from they boil down to this:

sudo cp autoreset /usr/bin
sudo cp avrdude-autoreset /usr/bin
sudo mv /usr/bin/avrdude /usr/bin/avrdude-original
sudo ln -s /usr/bin/avrdude-autoreset /usr/bin/avrdude

Next open the file /usr/bin/autoreset and change the reset pin to the pin you connected the Arduino reset to. The GPIO pin number corresponds to the number of the pin of the header.

vim /usr/bin/autoreset

On your computer

Download and install Arduino IDE go to the folder containing avrdude On OS X this most likely is /Applications/

cd /Applications/
mv avrdude avrdude-original
chmod +x avrdude