Hello EMBOSS team, I'm using EMBOSS 6.2.0 on Mac OS X 10.6.3 Snow Leopard:
$ embossversion Reports the current EMBOSS version number 6.2.0 I need to design some primers so I wanted to try the EMBOSS tool eprimer3, which as your documentation clearly explains requires me to install the 'primer3' program from the Whitehead Institute (specifically the primer3_core tool). I downloaded and compiled the latest version of primer3, version 2.2.2 beta (using the default, i.e. just "make", which seems to be fine - the Snow Leopard specific Makefile failed). It seems that EMBOSS eprimer3 does not like this: $ export EMBOSS_PRIMER3_CORE="/Users/xxx/Downloads/Software/primer3-2.2.2-beta/src/primer3_core" $ eprimer3 fasta::lupine.nu lupine.eprimer3 Picks PCR primers and hybridization oligos Error: Missing SEQUENCE tag Instead, I downloaded and compiled primer3 version 1.1.4 (using the defaults, i.e. just "make", there is no Snow Leopard specific Makefile included) and that seems to work: $ export EMBOSS_PRIMER3_CORE="/Users/xxx/Downloads/Software/primer3-1.1.4/src/primer3_core" $ eprimer3 fasta::lupine.nu lupine.eprimer3Picks PCR primers and hybridization oligos Picks PCR primers and hybridization oligos The eprimer3 output looks sensible too. My guess is that something in the recent primer3 alpha and beta releases of 2.x.x has changed since version 1.x.x and that EMBOSS needs to be updated to cope. Is this a known issue? Thanks, Peter C. _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss