If like me you would like to upload your sketches using the AVRISP mkII under Linux like you can easily do under OSX, I suggest the following procedure:
1. Add the following text to board.txt (located in the relative path hardware/arduino in your arduino installation folder)
jivedingo wrote it on arduino forum
############################################################## avrispmkii_168.name=AVRISP mkII w/ ATmega168 avrispmkii_168.upload.protocol=avrispmkii avrispmkii_168.upload.maximum_size=14336 avrispmkii_168.upload.speed=19200 avrispmkii_168.upload.using=avrispmkii avrispmkii_168.bootloader.low_fuses=0xff avrispmkii_168.bootloader.high_fuses=0xdd avrispmkii_168.bootloader.extended_fuses=0x00 avrispmkii_168.bootloader.path=atmega avrispmkii_168.bootloader.file=ATmegaBOOT_168_ng.hex avrispmkii_168.bootloader.unlock_bits=0x3F avrispmkii_168.bootloader.lock_bits=0x0F avrispmkii_168.build.mcu=atmega168 avrispmkii_168.build.f_cpu=16000000L avrispmkii_168.build.core=arduino ############################################################## avrispmkii_328.name=AVRISP mkII w/ ATmega328 avrispmkii_328.upload.protocol=avrispmkii avrispmkii_328.upload.maximum_size=30720 avrispmkii_328.upload.speed=57600 avrispmkii_168.upload.using=avrispmkii avrispmkii_328.bootloader.low_fuses=0xFF avrispmkii_328.bootloader.high_fuses=0xDA avrispmkii_328.bootloader.extended_fuses=0x05 avrispmkii_328.bootloader.path=atmega avrispmkii_328.bootloader.file=ATmegaBOOT_168_atmega328.hex avrispmkii_328.bootloader.unlock_bits=0x3F avrispmkii_328.bootloader.lock_bits=0x0F avrispmkii_328.build.mcu=atmega328p avrispmkii_328.build.f_cpu=16000000L avrispmkii_328.build.core=arduino ##############################################################
2. Backup arduino’s avrdude and use your local avrdude
It seams that the avrdude binary coming with arduino 018 distribution isn’t compiled with usb support.
If your remove it and link your local avrdude binary instead, upload using mkII works like a charm.
# apt-get install avrdude libusb
# cd /path/to/arduino/folder
# cd hardware/tools
# ln -s avrdude avrdude.without-usb-support
# ln -s `type avrdude | cut -d "(" -f 2 | cut -d ")" -f 1` avrdude
Then you will be able to select AVRISP mkII \w ATmega328 or AVRISP mkII \w ATmega168 from the tools>board menu.