avrpi
'avrpi' is a tool that makes it easier to talk to your AVR chip on the Raspberry Pi.
pi@raspberrypi ~ $ avrpi -h
Usage: avrpi [options] <filename>
[options] is any of the following:
-f <file> flash <file> flash <file> to avrpi board
-u <file> upload <file> upload <file> using caterina bootloader
-d <file> upload <file> upload <file> using Atmel DFU bootloader
-i info show info about chip
-r reset reset AVR chip
-b bootloader enter bootloader mode (HWB fuses set)
-m minicom start minicom on /dev/ttyACM0 @ 9600
-n screen start screen on /dev/ttyACM0 @ 9600
-h help show this info
-c config edit avrpi config file
-s show show config
Depending on what board you have selected in the setup menu, these settings are saved in '/etc/avrpi.cfg'
pi@raspberrypi ~ $ avrpi -s
Use 'avrpi -c' to edit settings:
board = avrpi328
chip = atmega328p
speed = 8000000
programmer = linuxgpio
port = /dev/ttyAMA0
baud = 9600
delay = 5
The 'port' and 'baud' settings apply to USART port that avrpi will use to communicate in 'screen' or 'minicom'. It's not used in programming with avrdude.
The 'delay' is the isp clock delay. Anything other than 0 adds the -i avrdude option. This is 5 by default, because it really helps with having error free transfers. Especially when changing fuse settings.