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

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Thu Nov 1 15:51:41 EDT 2007


Doesn't EMBOSS binaries live under 'bin'? Perhaps setting 
PATH=$ENV{PATH} to 'C:\EMBOSSwin\bin' or using this:

my $fuzznuc = $f->program('fuzznuc');
$fuzznuc->executable('C:\EMBOSSwin\bin\fuzznuc');

Adding .exe might be worth trying as well.

Mauricio.

Cook, Malcolm wrote:
> 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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-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM



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