The Arduino Yun has both an Arduino (Atmega32u4) environment and a Linux (Linino) environment.
StandardFirmataYun enables Firmata running on the Arduino environment to communicate with a Firmata client application running on the Linux environment.
Clone or download this repo into your Arduino sketch library, compile and upload it to your Arduino Yun board.
You will need to install Firmata v2.5.0 via the Arduino library manager if using Arduino v1.6.4+, or manually if using an older version of the Arduino IDE. See the instructions on the firmata/arduino repo.