[Fwd: Re: [Bioperl-l] bioperl-run for windows?]

[Scott Markel]

Chris,

I use EMBOSSwin with BioPerl.  Mostly it runs fine.  Two
things to watch out for.  The first is the use of /dev/null
for stderr.  The second is that Bio::Factory::EMBOSS::_program_list
specifically fails if the OS is MSWin or Mac.

Scott

Chris Fields wrote:

> There is an EMBOSS release for Windows, believe it or not.  It is 
> currently at v. 2.7.1 and can be found at:
> 
> http://perso.wanadoo.fr/ablavier/embosswin/embosswin.html
> 
> I have no idea if it will work with Bioperl, though.  Might be 
> interesting to try at some point.
> 
> Chris
> 
> At 04:18 PM 1/24/2005, you wrote:
> 
>> Some will work, and some won't. I've installed it on Windows, and used it
>> a bit there. One problem you'll run into is that you can't use bioperl
>> to run a program that can't be installed on Windows (EMBOSS for 
>> example) so you'll
>> be limited that way, but check out the Pise interface for any of that
>> software. You should be able to get access to alot of non-windows
>> software via bioperl by using the Pise interface (
>>
>> Bio::Tools::Run::AnalysisFactory::Pise
>>
>> http://www.pasteur.fr/recherche/unites/sis/Pise/
>>
>>
>> Barry
>>
>> Tim Alcon wrote:
>>
>> > If I just grab it off CPAN, will it work on Windows, or does it use
>> > Unix system calls?
>> >
>> > Tim
>> >
>> >
>> >
>> > Jason Stajich wrote:
>> >
>> >> Is there a PPM on the bioperl site?
>> >> No
>> >>
>> >> Can you install bioperl-run on windows?
>> >> Yes - but you'll have to do it manually, or learn how to build PPMs
>> >> (quite simple really), or encourage someone to produce a PPM for
>> >> bioperl-run.
>> >>
>> >> -jason
>> >> On Jan 22, 2005, at 7:57 PM, Tim Alcon wrote:
>> >>
>> >>> Does a Windows version of bioperl-run exitst? If so, how do I get it?
>> >>>
>> >>> Tim
>> >>>
>> >>>
>> >>> _______________________________________________
>> >>> Bioperl-l mailing list
>> >>> Bioperl-l at portal.open-bio.org
>> >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>> >>>
>> >>>
>> >> --
>> >> Jason Stajich
>> >> jason.stajich at duke.edu
>> >> http://www.duke.edu/~jes12/
>> >>
>> >>
>> >
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at portal.open-bio.org
>> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> -- 
>> Barry Moore
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT
>>
>>
>>
>> -- 
>> Barry Moore
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> __________________________________
> 
> Chris Fields - Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> 
> Address:
> 
> University of Illinois at Urbana-Champaign
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> 
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-- 
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