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

Rohit Ghai Rohit.Ghai at mikrobio.med.uni-giessen.de
Thu Nov 1 05:45:43 EDT 2007


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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