[EMBOSS] problem with eprimer32

[Hamish McWilliam]

Hi folks,

> in the current EMBOSS there are 2 wrappers for eprimer:
> ####
> eprimer3     Pick PCR primers and hybridization oligos
> eprimer32    Pick PCR primers and hybridization oligos
> ####
> 
> eprimer3 is for primer3  version 2.3.x (works for me with 2.3.6) 
> and
> eprimer32 is for the older version 2.2.3
> 
> So if you want to use the new primer3 version (2.3.5), the symbolic link is not needed.
> Just put primer3_core in the path and use eprimer3.

FWIW you can set the path to the primer3_core version to use by setting
the corresponding environment variables in the EMBOSS configuration. For
example in my 'emboss.defaults' I have:

ENV EMBOSS_PRIMER3_CORE /ebi/extserv/bin/primer3-1.1.4/primer3_core
ENV EMBOSS_PRIMER32_CORE /ebi/extserv/bin/primer3-2.2.3/primer3_core

This method may make it somewhat easier to keep track of which versions
are being used that using the symlink and PATH options.

All the best,

Hamish

> 
> Kind regards,
> David.
> 
> -----Ursprüngliche Nachricht-----
> Von: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] Im Auftrag von Guy Bottu
> Gesendet: 13 February 2014 18:17
> An: emboss at lists.open-bio.org
> Betreff: [EMBOSS] problem with eprimer32
> 
> Dear all,
> 
> I installed on my computer EMBOSS version 6.6.0.0 and tried to make 
> eprimer32 work. I installed the last version of Primer3 (version 2.3.5) 
> and I put a logical link in the bin directory of EMBOSS (primer32_core 
> -> .../primer3_core). When I try to run it, I get :
> 
> Pick PCR primers and hybridization oligos
> Whitehead primer3_core program output file [emboss_001.eprimer32]:
> Error: thermodynamic approach chosen, but path to thermodynamic 
> parameters not specified
> 
> What could be missing ? The EMBOSS eprimer32 manual does not say 
> anything beyond the need to have eprimer3_core in the path.
> 
> Regards,
> Guy Bottu


-- 
============================================================
Mr Hamish McWilliam,
Web Production,
European Bioinformatics Institute (EMBL-EBI),
European Molecular Biology Laboratory,
Wellcome Trust Genome Campus,
Hinxton, Cambridge, CB10 1SD
United Kingdom

URL: http://www.ebi.ac.uk/
============================================================