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
Can I also expect the same problem with the external primer3 binary?
Presumably the same solution for clustal will work for primer3?
Also, and I suspect I know the answer to this question, I'm attempting
to input a test file into emma with the following contents:
SWISSPROT:PA1_HUMAN
SWISSPROT:PAX1_HUMAN
SWISSPROT:PAX2_HUMAN
SWISSPROT:PAX3_HUMAN
SWISSPROT:PAX4_HUMAN
SWISSPROT:PAX5_HUMAN
SWISSPROT:PAX6_HUMAN
SWISSPROT:PAX7_HUMAN
SWISSPROT:PAX8_HUMAN
SWISSPROT:PAX9_HUMAN
SWISSPROT:PAXI1_HUMAN
I pre-pended the path to this file with an @ to indicate that it's a
list file e.g.:
@C:\path\to\multiple\sequence\alignment\file.sw
Am I correct in assuming that even when I've resolved the path issue to
the clustalw binary, I need a locally installed database (or URL to an
external database) for this analysis to run successfully? If so, how do
I prepare/install/configure my system to access this database (Swiss-Prot)?
Many thanks for your time and help.
Best regards,
Nigel Binns
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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