[EMBOSS] specify primer3 directory?

[Scott Markel]

Paul,

Yup, sorry about that.  I should have stopped my answer after the paragraph about the primer3 change.

Scott


-----Original Message-----
From: ptanger at rams.colostate.edu [mailto:ptanger at rams.colostate.edu] On Behalf Of Paul Tanger
Sent: Thursday, 13 September 13 2012 2:59 PM
To: Scott Markel
Cc: emboss at lists.open-bio.org
Subject: Re: [EMBOSS] specify primer3 directory?

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 at 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.Markel at 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:  smarkel at accelrys.com
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>
> -----Original Message-----
> From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Paul Tanger
> Sent: Thursday, 13 September 13 2012 1:25 PM
> To: emboss at 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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