It can be confusing sometimes:). You seem to be using BioPerl, so, yes, you want to write your script according to the documentation for Bio::Tools::Primer3, which is part of the BioPerl distribution. The code that you posted, however, was written according to the documentation for BioPerl-Run, which is a different distribution altogether. You were going by Bio::Tools::Run::Primer3 instead of Bio::Tools::Primer3, which is the module that you want to use.

Update: You need to install primer3

In reply to Re^3: Primer3 - BioPerl by Khen1950fx
in thread Primer3 - BioPerl by blarsen20

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