[EMBOSS] question EMBOSS-GUI

[Luke McCarthy]

On Fri, 2003-10-24 at 05:10,
yann-francois.bizouerne at bayercropscience.com wrote:
> EMBOSS An error in ajfile.c at line 145: execvp ('getz -e '[TREMBL-id:Q977L9]'', NULL) failed: 'No such file or directory' Error:
> Unable to read sequence 'TREMBL-id:Q977L9' Died: seqret terminated: Bad value for '-sequence' with -auto defined seqret exited with
> status 1..

I replied to this messages off-list, but it describes a fairly common
problem (that will be dealt with when I bring the GUI up to speed for
EMBOSS 2.8.0), so I thought I'd reply here, too.

The problem in this case is that the getz application is not in the
GUI's PATH.  There are two solutions: 1) soft link whatever application
you need to the directory containing the rest of the EMBOSS
applications; 2) edit the statement on or about line 151 of GUI.pm and
add the required directory to the GUI's PATH.  The statement in question
looks like this:

	$ENV{'PATH'} = "$EMBOSS_BIN:/bin";

To add another directory, simply append it to the colon-separated list
on the right hand side of the assignment.  For example, if getz were
installed as /usr/bin/getz, you would edit the above statement to look
like this:

	$ENV{'PATH'} = "$EMBOSS_BIN:/bin:/usr/bin";

This solution applies to the SRS problem mentioned by the OP above, as
well as to a similar problem where emma fails to work because it can't
find clustalw.  Cheers,

Luke
-- 
Luke McCarthy
Research Officer, Bioinformatics
Department of Computer Science
University of Saskatchewan
mccarthy at cs.usask.ca