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

Chris Fields cjfields at uiuc.edu
Thu Nov 1 10:54:09 EDT 2007


This worked for me previously when I tested with WinXP on my old  
machine using EMBOSS v5:

ftp://emboss.open-bio.org/pub/EMBOSS/windows

I haven't tried it with EMBOSSWin (latest is v 2.7); it's probably  
better to use the latest EMBOSS version anyway so I suggest trying  
the version in the above link.  I'll test it again today and let you  
know what I find.

chris

On Nov 1, 2007, at 9:32 AM, 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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> jason at bioperl.org
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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