[Bioperl-l] bioperl / emboss on windows

Chris Fields cjfields at illinois.edu
Mon May 4 11:53:47 EDT 2009


Okay, so I assume everything works then?  I remember getting this to  
work at some point on WinXP years ago (I have since moved on to Linux/ 
Mac).

chris

On May 4, 2009, at 10:39 AM, uludag at ebi.ac.uk wrote:

>
> It looks like EMBOSS was disabled in Bio\Factory\EMBOSS.pm for Windows
> platform. After commenting out the related condition in the  
> _program_list
> function (as shown below) i don't get the "Application [needle] is not
> available" error any more.
>
>    if( #$^O =~ /MSWIN/i ||
>
> Regards,
> Mahmut
>
>
>> 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");
>
>
>
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