Treat $^O eq 'MSWin32' as Windows, and assume everything else is *nix.

Ran into the following error after attempting to run Bowtie 2.2.3 on FreeBSD 9.2:

```
$ bowtie2
(ERR): Expected bowtie2 to be in same directory with bowtie2-align:
/opt/bowtie/2.2.3/
Exiting now ...
```

On FreeBSD, the Perl <b>$^O</b> variable is 'freebsd', whereas the code assumes that everything that isn't 'linux' or 'darwin' is Windows.

Per http://www.perlmonks.org/?node_id=845088 , <b>$^O</b> is 'MSWin32' on all flavors of Windows; it would be more portable to assume everything that isn't Windows is *nix.