On Wed, Aug 11, 2010 at 2:31 PM, Nigel Binns <n.bi...@ed.ac.uk> wrote: > > Hi All, > > Please can anyone tell me why my installation of Jemboss (EMBOSS v6.3.1 > patch v1-4) can't find the external clustal binary and how to correct this. > When I run a multiple sequence alignment using emma, I get the following > output: > > Died: emma uses external program 'clustalw' which is not in the PATH or > defined as EMBOSS_CLUSTALW > > I can confirm that my jemboss.properties file > ($EMBOSS_ROOT/share/EMBOSS/jemboss/resource/jemboss.properties) correctly > points to the root directories of the clustalw and primer3 binaries e.g.: > > embossPath=/path/to/clustal:/path/to/primer3
Have you got clustalw 1.x or 2.x installed? The binary names differ, clustalw.exe versus clustalw2.exe (no extension on Unix/Linux), and perhaps EMBOSS only expects the former? Have you tried setting the EMBOSS_CLUSTALW variable? Peter _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss