Question

Is it somehow possible to run git-annex on windows?

Answer 1

Update 2013/2014: as mentioned below by Abbafei, there is a beta version (as of Oct. 2014) for Windows.

version 5.20140221

The Windows port of the assistant and webapp is now considered to be beta quality. There are important missing features (notably Jabber), documented on windows support, but the webapp is broadly usable on Windows now.

The most recent update for Windows (day 219, Sept. 13th, 2014), mentions:

Windows support improved more than I guessed in my wildest dreams.

git-annex went from working not too well on the command line to being pretty solid there, as well as having a working and almost polished webapp on Windows.
There are still warts — it’s Windows after all!

So the situation is improving, but that remains a work in progress.

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Original answer (June 2011)

That recent thread (March 2011) doesn’t leave much hope:

Well, I can tell you that it assumes a POSIX system, both in available utilities and system calls, So you’d need to use cygwin or something like that. (Perhaps you already are for git, I think git also assumes a POSIX system.) So you need a Haskell that can target that.
What this page refers to as “GHC-Cygwin“: I don’t know where to get one.
Did find this thread.
(There are probably also still some places where it assumes / as a path separator, although I fixed some.)
FWIW, git-annex works fine on OS X and other fine proprietary unixen. ;P

You also find that coment in this bug report (March 2011):

Currently the hashed directories in .git-annex allow for upper and lower case directory names… on linux (or any case sensitive filesystem) the directory names such as ‘Gg‘ and ‘GG‘ are different and unique.
However on systems like OSX (and probably windows if it is ever supported) the directory names ‘Gg‘ is the same as ‘GG‘