[Bioperl-l] PRIMER_THERMODYNAMIC_PARAMETERS_PATH

[Fields, Christopher J]

If you are running a newer version of Primer3 you must use the Bio::Tools::Primer3Redux distribution (which also contains a modified wrapper, Bio::Tools::Run::Primer3Redux).  The reason was the original module had some fundamental issues that were never addressed and required a rewrite, but since there were issues with backwards-compatibility (and I needed something to work yesterday) I rewrote it.

The code is on CPAN and have very few requirements beyond bioperl (of course):

https://metacpan.org/release/Bio-Tools-Primer3Redux

chris

On Apr 17, 2013, at 11:32 AM, Veronica A. <armendarez77 at hotmail.com> wrote:

> Hello,
> I've just updated to bioperl-run (1.006900) and perl (v5.14.2) installed on a Linux machine running Ubuntu 12.04.
> I have perl scripts that use Bio::Tools::Run::Primer3 and before the updates, ran as expected.  However, they are now failing.
> While testing primer3_core on the command line, I realized the problem was the PRIMER_THERMODYNAMIC_PARAMETERS_PATH setting.  I added this to my primer3_core input file and primers were designed.  I.T. then moved the primer3_config directory to /opt/primer3_config as instructed and this helped running primer3_core on the command line as I no longer needed to include PRIMER_THERMODYNAMIC_PARAMETERS_PATH to the input file.  However, the perl scripts still do not work.
> Is there a BioPerl config file that requires the PRIMER_THERMODYNAMIC_PARAMETERS_PATH setting?  Or did something not install correctly?
> Thank you,
> Veronica 		 	   		  
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