Avrdude

For ATMega168:

$ avrdude -c buspirate -P /dev/ttyUSB1 -x speed=3 -p m168

For ATMega328p:

$ avrdude -c buspirate -P /dev/ttyUSB1 -x speed=3 -p m328p

Terminal mode: -t. Use command part to see detailed part information.
To upload file: -U memtype:op:filename[:format]
To use the arduino bootloader: -c stk500v1