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

[Jason Stajich]

Presumably the PATH is not getting set properly - you should play  
around printing the $ENV{PATH} variable in a perl script to see if  
actually contains the directory where the emboss programs are  
installed.  Bioperl can only guess so much as to where to find an  
application.  It is also possible that we aren't creating the proper  
path to the executable - you can print the executable path with
print $fuzznuc->executable
I believe unless it is throwing an error at the program() line.

It looks like the code in the Factory object is a little fragile  
assuming that the programs HAVE to be in your $PATH.  I don't know if  
windows+perl is special in any way that it run things so I can't  
really tell if there is specific things you have to do here. You may  
have to run this through cygwin in case PATH and such are just not  
available properly to windowsPerl.

-jason
On Nov 1, 2007, at 5:45 AM, Rohit Ghai wrote:

> 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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--
Jason Stajich
jason at bioperl.org