[Bioperl-l] PRIMER_THERMODYNAMIC_PARAMETERS_PATH

[Veronica Armendarez]

Thank you.
On Apr 17, 2013 6:30 PM, "Fields, Christopher J" <cjfields at illinois.edu>
wrote:

> 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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