The following programming instructions are a work in progress, so let us know if you have anything to add or modify.

######### To program a hex file from the Windows command line:

If you have previously installed Atmel Studio, then uninstall the driver it installed. Device Manager -> Jungo -> ??mkII -> uninstall

Download the AVR zip file (at the bottom of the "Assignments" page
Extract the files to some directory of your choice.
Plug your battery pack into your breadboard
Plug in the USB (to your PC) 
	Don't let Windows install the driver if it asks you to
Run zadig.exe
	Change the driver to libusb-win32 (v1.2.6.0)
	Install the driver
	The driver should show up in the Device Manager
		under libusb-win32 devices as AVRISP mkII
	
Open the file "command.txt" (one of those in the zip file) in a notepad 
Open a "Command Window" (Type "cmd" from the start menu)
cd to the directory containing avrdude (directory your extracted files to)
Execute the line in "command.txt" (easiest to cut and paste it).




######### Linux (Ubuntu)

$ sudo apt-get install bison flex byacc libudev-dev
compile and install libusb:
	download
	cd to directory
	$ ./configure
	$ make
	$ sudo make install

	
######### Linux (Fedora)

$ sudo dnf install avrdude bison flex byacc systemd-devel libusb libusb-devel
Download avr.zip from course website
Extract the zip to its own folder
Download http://download.savannah.gnu.org/releases/avrdude/avrdude-6.2.tar.gz
Copy the tar to the same folder to which you extracted avr.zip 
$ tar xf avrdude-6.2.tar.gz
$ cp endpointdetect_pass1.patch avrdude-6.2
$ cd avrdude-6.2 
$ patch < endpointdetect_pass1.patch
$ ./configure
$ make
$ sudo make install