If you have your temp dir on an unordinary place, just do this:

BEGIN { $TempFile::TMPDIRECTORY = '/mytmp' }
use CGI;
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Or edit your CGI.pm in the right place:

# HARD-CODED LOCATION FOR FILE UPLOAD TEMPORARY FILES.
# UNCOMMENT THIS ONLY IF YOU KNOW WHAT YOU'RE DOING.
# $TempFile::TMPDIRECTORY = '/usr/tmp';
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--
tune