I set my env path to C:\cygwin\bin, but that didn't help.

I hypothesis that you *think* you did. If either of the following work, you didn't.

my $length = `c:\\cygwin\\bin\\wc -l < $ARGV[0]/DAT/metadata.dat`;
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$ENV{PATH} = "$ENV{PATH};c:\\cygwin\\bin";
my $length = `wc -l < $ARGV[0]/DAT/metadata.dat`;
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Did you use [ Right click on My Computer | Properties | Advanced | Environment Variables ] as you need to?

Did you restart Komodo afterwards?