On Thu, Aug 12, 2010 at 9:17 AM, Nigel Binns <n.bi...@ed.ac.uk> wrote: > > Hi Peter, > > Many thanks for your reply. I have ClustalW v2 installed (v2.0.12 - the > latest release). The binary is named clustalw2. However, as I understand it, > when running the Jemboss installation script, you are asked to provide the > root directory that contains the clustalw binary rather than the name of the > actual binary i.e /path/to/clustal/root/ rather than > /path/to/clustal/root/clustalw2 or have I got that wrong?
I was suggesting the problem could be EMBOSS only looks for clustalw and not clustalw2. > The same issue applies to my installation of Primer3 ( latest release - > 3-2.2.2-beta). The binary name is primer3_core. I get this error when I try > to run eprimer3. > > Error application terminated > > Died: eprimer3 uses external program 'primer3_core' which is not in the > PATH or defined as EMBOSS_PRIMER3_CORE > Part of the 'primer3' package, version 3.0, available from the > Whitehead Institute. See: http://primer3.sourceforge.net/ > > Please can you tell me what file I should set the EMBOSS_CLUSTALW and > EMBOSS_PRIMER3_CORE variables in. They are just environment variables (set up in the OS), but I haven't ever used Jemboss so don't know how it would handle this. > > Many thanks for your help. > > Nigel Peter C. _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss