[Bioperl-l] bioperl: cannot run emboss programs using bioperl onwindows

Kevin Brown Kevin.M.Brown at asu.edu
Thu Nov 1 13:25:30 EDT 2007


Sounds like a path issue.  Try to tell bioperl the full path to the
executable rather than just the executable name. 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Rohit Ghai
> Sent: Thursday, November 01, 2007 2:46 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] bioperl: cannot run emboss programs 
> using bioperl onwindows
> 
> Dear all,
> 
> I have emboss installed on a windows machine. (Embosswin). I can run
> this from the dos command line and the path is present. 
> However, when I 
> try to call
> an emboss application from bioperl I get a "Application not 
> found error"
> 
> 
>   my $f = Bio::Factory::EMBOSS->new();
>   # get an EMBOSS application  object from the factory
>   my $fuzznuc = $f->program('fuzznuc');
>     $fuzznuc->run(
>                   { -sequence  => $infile,
>                         -pattern   => $motif,
>                        -outfile   => $outfile                       
>               });
>  gives the following error
> 
> -------------------- WARNING ---------------------
> MSG: Application [fuzznuc] is not available!
> ---------------------------------------------------
> Can't call method "run" on an undefined value at 
> searchPatterns.pl line 
> 102.
> 
> Can somebody help me fix this ?
> 
> best regards
> Rohit
> 
> -- 
> 
> Dr. Rohit Ghai
> Institute of Medical Microbiology
> Faculty of Medicine
> Justus-Liebig University
> Frankfurter Strasse 107
> 35392 - Giessen
> GERMANY
> 
> Tel  :	0049 (0)641-9946413
> Fax  :	0049 (0)641-9946409
> Email:  Rohit.Ghai at mikrobio.med.uni-giessen.de
> 
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> 



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