[EMBOSS] Question about Emma using emboss-GUI

[Luke McCarthy]

On Fri, 2003-08-08 at 06:24, Jean Mao wrote:
> Hi, 
> I installed the Emboss-GUI and are testing it. I got an error message
> when I tried emma using the GUI web interface. The error message says:
> EMBOSS An error in ajsys.c at line 360: cannot find program 'clustalw'
> emma exited with status 1...
> However, I got no error when I tried emma on the command line. Would
> you help me? Thank you very much.

If you are using my EMBOSS::GUI, it is very likely that clustalw is not
in the GUI's path.  For security reasons, the GUI assumes a very strict
path: normally just the directory containing the EMBOSS binaries and
/bin (because one of the EMBOSS programs requires ls...)

If this is the problem, there are a couple of solutions: first, you can
link or move clustalw to the same directory as the rest of the EMBOSS
binaries; second, you can add the directory containing clustalw to the
GUI's path.  If you decide to go the second route, you'll have to edit
the GUI.pm module in a minor way, so email me off-list and I'll give you
directions.  In most situations, however, the first way is easier by
far.

Cheers,

Luke

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