Paul, Yup, sorry about that. I should have stopped my answer after the paragraph about the primer3 change.
Scott -----Original Message----- From: ptan...@rams.colostate.edu [mailto:ptan...@rams.colostate.edu] On Behalf Of Paul Tanger Sent: Thursday, 13 September 13 2012 2:59 PM To: Scott Markel Cc: emboss@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@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! > _______________________________________________ > EMBOSS mailing list > EMBOSS@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > > _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss