I have not tried this, since I usually use a text editor for Perl, but I took the line shebang #!/usr/bin/env perl to use to get perl for the user who runs the script (i.e. perlbrew, if me, perl system if root). If Eclipse runs the script ( ./myscript.pl) this should work, if instead it calls perl myscript.pl ", this will not help you.
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