I will add more detail hopefully soon, just in case the links go dead.
Watch for " the inverted commas, I had some issue with these.
Guide:
- Select Tools > External Tools
- Then fill the details in window as show in the screenshot
########### Workings out for setting avrdude in Atmel Studio ####
for use with assembler uploading hex file
http://www.avrfreaks.net/index.php?name=PNphpBB2&file=viewtopic&p=1158681
http://asensar.com/2013/06/23/programming-arduino-using-avrdude/
http://asensar.com/2013/06/23/how-to-integrate-avrdude-with-atmel-studio/
### initial output from Arduino
Binary sketch size: 1,084 bytes (of a 32,256 byte maximum)
\\path\Arduino
\hardware/tools/avr/bin/avrdude -C\\path
\Arduino\hardware/tools/avr/etc/avrdude.conf -v -v -v -v -patmega328p -carduino -P\
\.\COM6 -b115200 -D -Uflash:w:C:\Users\user\AppData\Local\Temp
\build4700042702866457239.tmp\Blink.cpp.hex:i
## simplifying the above output
avrdude -C\\path\Arduino
\hardware/tools/avr/etc/avrdude.conf -v -v -v -v -patmega328p -carduino -P\\.\COM6
-b115200 -D -Uflash:w:<myhexfile>:i
uno.name=Arduino Uno
uno.upload.protocol=arduino
uno.upload.maximum_size=32256
uno.upload.speed=115200
uno.bootloader.low_fuses=0xff
uno.bootloader.high_fuses=0xde
uno.bootloader.extended_fuses=0x05
uno.bootloader.path=optiboot
uno.bootloader.file=optiboot_atmega328.hex
uno.bootloader.unlock_bits=0x3F
uno.bootloader.lock_bits=0x0F
uno.build.mcu=atmega328p
uno.build.f_cpu=16000000L
uno.build.core=arduino
uno.build.variant=standard
## copy of other chaps. needed tweaking. paths etc
-F -v -patmega328p -carduino -P.COM6 -b115200 -D -Uflash:w:"$(ProjectDir)Debug\
$(ItemFileName).hex":i -C\\path\Arduino
\hardware/tools/avr/etc/avrdude.conf
