Probably you should first try a precompiled binary.

If that doesn't work, another more complicated option is compiling atlas under Windows, using cygwin, the Windows linux emulator.

(1) Download cygwin: download setup.exe from www.cygwin.com.

(2) Install cygwin: Double-click on setup.exe to run it. At the package menu choose at least the following packages:

1. gcc/g++ (version 4x)
2. make
3. bison
4. libncurses-devel
5. libstdc++6-devel
6. readline
7. git (optional)
8. texlive (optional)

(3) Open a cygin terminal by double-clicking on the icon. You are now in a linux-like environment.

(4) Follow the instruction on the linux page.