If you are using a fresh install of Retropie you will need to manually install the Joystick and Buttons.
Login to your Raspberry Pi via Putty
Download Retrogame
curl https://raw.githubusercontent.com/adafruit/Raspberry-Pi-Installer-Scripts/master/retrogame.sh >retrogame.sh
Install Retrogame
sudo bash retrogame.sh
When run, you’ll be asked to pick one of several control configurations. It doesn't matter which one you choose as we will be editing the install to fit our needs. For now, select 6. Once install is complete you will be asked to reboot. Do not reboot at the moment.
Edit the retrogame.cfg file
sudo nano /boot/retrogame.cfg
Replace the contents with the following:
# ZEGAMAMEGEAR - DESKTOP ARCADE INPUT CONFIGURATION LEFT 25 # Joypad left RIGHT 12 # Joypad right UP 17 # Joypad up DOWN 24 # Joypad down LEFTCTRL 6 # 'A' button LEFTALT 20 # 'B' button Z 5 # 'X' button X 16 # 'Y' button SPACE 26 # 'Select' button ENTER 13 # 'Start' button
Save your changes and Reboot
sudo reboot
You will now need to configure the input to assign your Desktop Arcade buttons and Joystick.