[Bioperl-l] bioperl / emboss on windows

Scott Markel SMarkel at accelrys.com
Mon May 4 09:41:06 EDT 2009


Is needle in your path?

Note that needle needs two input sequences, which you don't provide.
You might try invoking embossversion, which takes no inputs.

Scott

Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at accelrys.com
Accelrys (SciTegic R&D)             mobile: +1 858 205 3653
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Vice President, Board of Directors:
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> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of yi wang
> Sent: Sunday, 03 May 2009 9:43 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] bioperl / emboss on windows
> 
> ---------- Forwarded message ----------
> From: yi wang <wangyi2412 at gmail.com>
> Date: 2009/5/4
> Subject: bioperl on windows
> To: bioperl-l at bioperl.org
> 
> 
> I have installed the bioperl and emboss on my* windows xp*, as guided on
> the web. But it
> --------------------- WARNING ---------------------
> *MSG: Application [needle] is not available!*
> ---------------------------------------------------
> 
> 
> use warnings;
> use CGI;
> use Bio::Perl;
> use Bio::Root::Root;
> use Bio::Factory::ApplicationFactoryI;
> use Bio::Factory::EMBOSS;
> use Bio::Tools::Run::EMBOSSApplication;
> 
> 
> 
> *my $f = Bio::Factory::EMBOSS -> new();*
> *$f->program("needle");*
> #my $factory = new Bio::Factory::EMBOSS; #my $compseqapp = $factory-
> >program("needle");
> 
> I checked the manual and the emboss.pm, write the programe as the demo,
> but it could work! How could it be the problem? Thank you very much!
> *Looking for your reply!*
> 
> 
> Best Wishes,
> 
> 
> 
> --
> ºÍÄãÔÚÒ»Æð




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