The following configuration works for flashing the Arduino Uno with the AVRISP MKII:
[env:uno] platform = atmelavr board = uno framework = arduino upload_protocol= custom upload_port = usb upload_flags = -C $PROJECT_PACKAGES_DIR/tool-avrdude/avrdude.conf -p $BOARD_MCU -P $UPLOAD_PORT -c avrispmkII ; -c stk500v2 upload_command = avrdude $UPLOAD_FLAGS -U flash:w:$SOURCE:i