Assuming you already have a binary file for flashing, this page may help you. All you need to do is:
Connect target the Arduino with loaded ArduinoISP sketch to the target chip
Run AVRDude. Make sure to specify a programmer type. Also note that ArduinoISP will work at lower serial speeds. Example:
avrdude -p m328p -P /dev/ttyACM0 -c avrisp -b 19200 -U flash:w:release.hex