I wouldn't recommend trying to run ABySS on cygwin -- I've never tested it and it's not a platform that we officially support. You will have far less problems on Linux/Mac, and I think you will find the story is the same for the majority of bioinformatics software. If you are really set on using Windows as your O/S then I would recommend setting up a virtual machine running Linux (e.g. Ubuntu) with VirtualBox or VMWare instead of using cygwin.

That said, if you want to try installing ABySS on cygwin anyway:

1. download the source tarball here: http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.0.0
2. unpack it: run tar xvf abyss-2.0.0.tar.gz in the download directory.
3. cd abyss-2.0.0
4. ./configure
5. make
6. make install

See https://github.com/bcgsc/abyss#compiling-abyss-from-source for more info.

Good luck!

I agree with benv. I would recommend either setting up a VirtualBox VM (where you can have an Unbuntu graphical interface).

https://www.virtualbox.org/wiki/Downloads

http://www.ubuntu.com/download/desktop

Installing Docker might also be a good option, where some other programs are even "Dockerized" (where you can download an image with the program already installed)

https://www.docker.com/products/docker-toolbox

https://docs.docker.com/engine/getstarted/