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-boun...@lists.open-bio.org > [mailto:emboss-boun...@lists.open-bio.org] Im Auftrag von Guy Bottu > Gesendet: 13 February 2014 18:17 > An: emboss@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/ ============================================================ _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss