Thanks, maybe this is the problem but the solution you suggest doesn't
seem to work because that is a primer3 qualifier not an eprimer3
qualifier.
I get this error:
[paultanger@bspmgenomics bin]$ ./eprimer3
~/QTL-project/30scaffolds_affyMAI_CG.fsa ~/QTL-project/test2
--default_version=1
Died: Unknown qualifier --default_version=1
On Thu, Sep 13, 2012 at 3:49 PM, Scott Markel <scott.mar...@accelrys.com> wrote:
> Paul,
>
> You might want to have a look at section 5 of the primer3 documentation
> ("CHANGES FROM VERSION 2.2.3"). They changed the default for
> PRIMER_THERMODYNAMIC_ALIGNMENT from 0 to 1. If this is left at 1, then you
> also need to supply a value for PRIMER_THERMODYNAMIC_PARAMETERS_PATH.
>
> You can revert to the old defaults using this command-line argument.
>
> --default_version=1
>
> Scott
>
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect email: smar...@accelrys.com
> Accelrys (Pipeline Pilot R&D) mobile: +1 858 205 3653
> 10188 Telesis Court, Suite 100 voice: +1 858 799 5603
> San Diego, CA 92121 fax: +1 858 799 5222
> USA web: http://www.accelrys.com
>
> http://www.linkedin.com/in/smarkel
> Secretary, Board of Directors:
> International Society for Computational Biology
> Chair: ISCB Publications and Communications Committee
> Associate Editor: PLoS Computational Biology
> Editorial Board: Briefings in Bioinformatics
>
>
> -----Original Message-----
> From: emboss-boun...@lists.open-bio.org
> [mailto:emboss-boun...@lists.open-bio.org] On Behalf Of Paul Tanger
> Sent: Thursday, 13 September 13 2012 1:25 PM
> To: emboss@lists.open-bio.org
> Subject: [EMBOSS] specify primer3 directory?
>
> Hi,
> I have a local install of emboss and I'm trying to get eprimer3 to
> work, but I'm getting this error:
>
> "Error: thermodynamic approach chosen, but path to thermodynamic
> parameters not specified"
>
> primer3 is installed, but not in the default location (which I think
> is /opt/primer3_config ?) .
> How do I specify where primer3 is installed? Or is the cause of this
> error something else?
>
> googled for an answer for a while, but couldn't find one.
>
> Thanks!
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> EMBOSS@lists.open-bio.org
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>
>
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