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.

Ah yes, this was mentioned to me earlier this morning as well! Shame, I actually had never heard it mentioned before! :: facepalm ::

Much appreciated! Also should help now that it's been moved to a server and off windows! Joy! Haha

For some reason it didn't really put my reply yesterday... But yeah, someone actually mentioned that yesterday! Never knew we had to download two separate packages. :: facepalm :: So, I have it running but receive an error (see the "UPDATE" in the main post).

The error I get as soon when dumping the results data structure via:

 my $results = $primer3->run;
print Dumper($results);
[download]

is "'PRIMER_ERROR' => 'thermodynamic approach chosen, but path to thermodynamic parameters not specified'". Not sure as to why this is, especially since it looks like that is not the default and I never passed anything in like that...hmm. Trying to modify it still, but got that error multiple times yesterday.