I use a tinyISP and the arduino IDE to burn the bootloader and on the beagle I did:

root@cyclops:~# avrdude -cstk500v1 -b57600 -patmega328p  -P/dev/ttyS1 -C /etc/avrdude.conf  -U flash:w:mendel.hex

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.02s

avrdude: Device signature = 0x1e950f
avrdude: NOTE: FLASH memory has been specified, an erase cycle will be performed
        To disable this feature, specify the -D option.
avrdude: erasing chip
avrdude: reading input file "mendel.hex"
avrdude: input file mendel.hex auto detected as Intel Hex
avrdude: writing flash (14018 bytes):

Writing | ################################################## | 100% 5.14s

avrdude: 14018 bytes of flash written
avrdude: verifying flash memory against mendel.hex:
avrdude: load data flash data from input file mendel.hex:
avrdude: input file mendel.hex auto detected as Intel Hex
avrdude: input file mendel.hex contains 14018 bytes
avrdude: reading on-chip flash data:

Reading | ################################################## | 100% 4.27s

avrdude: verifying ...
avrdude: 14018 bytes of flash verified

avrdude: safemode: Fuses OK

avrdude done.  Thank you.

And when that was finished I tried to see if the firmware was running:

root@cyclops:~# cat /dev/ttyS1 &
root@cyclops:~# echo M115 > /dev/ttyS1
root@cyclops:~# ok FIRMWARE_NAME:FiveD_on_Arduino FIRMWARE_URL:http%3A//github.com/triffid/FiveD_on_Arduino/ PROTOCOL_VERSION:1.0 MACHINE_TYPE:Mendel EXTRUDER_COUNT:1 HEATER_COUNT:1