Included javascript with perl

The reason included javascript (i.e. <script type="text/javascript" src="file.js">) does not work, is because must likely the "file.js" was placed in a directory that was configured as cgi. If you move the file outside the cgi path then you can reference it and it will work. ex. I moved my script file from:
/var/www/cgi-bin/apps/file.js to
/var/www/js/file.js....