2.5 years ago by
I just attempted this and had a ton of trouble getting wheels (Galaxy's python dependencies) built on Cygwin. psutil is the dependency that flat out says "cygwin is not supported", so I disabled that and went through and installed the -dev packages for the various components to hopefully build the rest of things, but I still ran into many problems.
I'd really recommend that a much better path to using Galaxy on windows would be to use Docker (https://github.com/bgruening/docker-galaxy-stable), or (and this is what I do) install VirtualBox www.virtualbox.org) and set up a barebones linux machine that you can run using Xubuntu or some similarly lightweight distro. Let me know if I can give any other advice about this!