[Bioperl-l] Re: Can't locate clustalw

[Hilmar Lapp]

Peter Schattner wrote:
> 
> Hilmar Lapp wrote:
> >
> > (Instead, the clustalw
> > test does not [work], because it appears to reference the non-existent
> > /home/peter/clustalw1.8/clustalw. I don't know what's the correct name of
> > the file or directory.)
> > --
> 
> or
> 3. Modify your $PATH variable to include your clustalw directory as in
> (for bash):
>         export PATH=$PATH:/home/peter/clustalw1.8
> 

Well, this wouldn't have worked because you explicitely check for and set
CLUSTALDIR in the test script, even though the module already takes care
of this properly. I fixed it, and I fixed also the detection code in
Clustalw.pm, because in fact it didn't report that clustalw is missing on
my machine. The problem is probably that there is no error message, hence
$@ being empty. The code now checks for $? being zero. This is a problem
if 'clustalw -options' returns a non-zero exit status.

	Hilmar

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Hilmar Lapp                                email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
A-1235 Vienna                                fax: +43 1 86634 727
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