Bowtie.t: "qx/ulimit -n 3>&-/" does not work as intended on Windows;
even though "ulimit" command doesn't exists, $ulimit is defined but
empty, $@ is not set, and the OS doesn't understand "&-". So using
a fixed number for Windows.
Hmmer: Prevent errors caused by the presence of whitespace
in paths by adding double quotes if detected before running
the program. Also in Windows NUL is the equivalent of /dev/null
Added a way to find the required files in Windows using "dir"
Windows use 'NUL' instead of '/dev/null', so added the option
to use it when running in Windows