[Bioperl-l] bioperl: cannot run emboss programs usingbioperlonwindows

Cook, Malcolm MEC at stowers-institute.org
Thu Nov 1 14:57:33 EDT 2007


in the code
http://doc.bioperl.org/bioperl-run/Bio/Factory/EMBOSS.html#CODE6 

there is a call to `wossname` (c.f.
http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/wossname.html
)

is wossname in your path?

Maybe it needs to be wossname.exe under windows?


Malcolm Cook
  

> -----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 1:42 PM
> To: Jason Stajich
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] bioperl: cannot run emboss programs 
> usingbioperlonwindows
> 
> Hi Jason
> 
> I tried this as well. This also gives the same error message.
> 
> -Rohit
> 
> Jason Stajich wrote:
> > You could try this - can't test it though so not sure.
> > my $fuzznuc = $f->program('fuzznuc');
> > $fuzznuc->executable('C:\EMBOSSwin\fuzznuc');
> >
> > -jason
> > On Nov 1, 2007, at 2:06 PM, Rohit Ghai wrote:
> >
> >>
> >>
> >> Thanks for all the suggestions... but I unfortunately still cannot 
> >> run emboss. I am running the latest version of embosswin  
> >> (2.10.0-Win-0.8), and the path is set correctly. I printed 
> >> $ENV{$PATH} and this contains C:\EMBOSSwin which is the correct 
> >> location.
> >> I also tried setting the path directly but I'm not sure how to do 
> >> this, so I tried this...
> >>
> >> my $fuzznuc = $f->program('C:\\EMBOSSwin\\fuzznuc');
> >>
> >> this also did not work.
> >>
> >> Also tried printing...
> >> $fuzznuc->executable()
> >>
> >> gave the following error again
> >> -------------------- WARNING ---------------------
> >> MSG: Application [C:\EMBOSSwin\fuzznuc] is not available!
> >> ---------------------------------------------------
> >>
> >> Any more ideas ?
> >>
> >> thanks !
> >> Rohit
> >>
> >>
> >> here's the code...
> >>
> >> use strict;
> >> use Bio::Factory::EMBOSS;
> >> use Data::Dumper;
> >>
> >> #
> >> # print "PATH=$ENV{PATH}\n";
> >> # path contains C:\EMBOSSwin which is the correct location # 
> >> embossversion is 2.10.0-Win-0.8
> >>
> >>  my $f = Bio::Factory::EMBOSS->new();  # get an EMBOSS 
> application  
> >> object from the factory  print Dumper ($f);  my $fuzznuc = 
> >> $f->program('C:\\EMBOSSwin\\fuzznuc'); #tried fuzznuc.exe 
> as well,  
> >> print Dump ($fuzznuc);
> >>
> >>  #dump of fuzznuc
> >>  #$VAR1 = bless( {
> >>  #                '_programgroup' => {},
> >>  #                '_programs' => {},
> >>  #                '_groups' => {}
> >>  #              }, 'Bio::Factory::EMBOSS' );
> >>
> >>  #print "executing -- >", $fuzznuc->executable, "\n" ; # 
> doesn't work
> >>
> >>  my $infile = "temp.fasta";
> >>  my $motif  = "ATGTCGATC";
> >>  my $outfile = "test.out";
> >>
> >>
> >>  $fuzznuc->run(
> >>                   { -sequence  => $infile,
> >>                     -pattern   => $motif,
> >>                     -outfile   => $outfile                      
> >>               });
> >>
> >> Here's the error again....
> >>
> >> #-------------------- WARNING ---------------------
> >> #MSG: Application [C:\EMBOSSwin\fuzznuc] is not available!
> >> #---------------------------------------------------
> >>
> >>
> >>
> >>
> >> Jason Stajich wrote:
> >>> 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
> >>>> <mailto:Rohit.Ghai at mikrobio.med.uni-giessen.de>
> >>>> <mailto:Rohit.Ghai at mikrobio.med.uni-giessen.de>
> >>>>
> >>>> _______________________________________________
> >>>> Bioperl-l mailing list
> >>>> Bioperl-l at lists.open-bio.org 
> <mailto:Bioperl-l at lists.open-bio.org>
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>> --
> >>> Jason Stajich
> >>> jason at bioperl.org <mailto:jason at bioperl.org>
> >>>
> >>
> >> --
> >>
> >> 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
> >> <mailto:Rohit.Ghai at mikrobio.med.uni-giessen.de>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org <mailto:Bioperl-l at lists.open-bio.org>
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > --
> > Jason Stajich
> > jason at bioperl.org <mailto:jason at bioperl.org>
> >
> 
> -- 
> 
> 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
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



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