[Bioperl-l] bioperl: cannot run emboss programs usingbioperlonwindows
Mauricio Herrera Cuadra
arareko at campus.iztacala.unam.mx
Thu Nov 1 19:51:41 UTC 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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