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.

I'm getting this same error on my mac osx build. Any luck solving this issue?

Primer3/eprimer3 issue:
Error: thermodynamic approach chosen, but path to thermodynamic parame
+ters not specified
[download]

From: http://www.mcardle.wisc.edu/mprime/help/primer3/primer3_manual.htm#globalTags

PRIMER_THERMODYNAMIC_PARAMETERS_PATH (string; default ./primer3_config)

This tag specifies the path to the directory that contains all the parameter files used by the thermodynamic approach. In Linux, there are two default locations that are tested if this tag is not defined: ./primer3_config/ and /opt/primer3_config/. For Windows, there is only one default location: .\primer3_config\.

I put the primer3_config in my PATH in bin and still cannot solve this issue:

I even did

export PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/Users/jared/Downloads/pri
+mer3-2.3.2/src
[download]

and

export PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/Users/jared/Downloads/pri
+mer3-2.3.2/src/primer3_config
[download]

to no avail.