[Bioperl-l] bioperl / emboss on windows

Chris Fields cjfields at illinois.edu
Mon May 4 12:30:23 EDT 2009


Yes, I recall something along those lines.  Parameters are something  
that need to be genericized for EMBOSS use.  Good to hear it works,  
though.

chris

On May 4, 2009, at 11:26 AM, uludag at ebi.ac.uk wrote:

>
>> 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).
>
> I cannot say everything works but it looks like at least basic  
> things are
> working. I just tested the 'water' example given on top of EMBOSS.pm.
> Example Bio::Seq inputs were properly transferred to 'water' and  
> bioperl
> was able to construct Bio::AlignIO object from the output file EMBOSS
> generated.
>
> In the example, 'water' inputs are named as 'sequencea' and 'seqall',
> however, i needed to rename them as 'asequence' and 'bsequence' (i use
> mEMBOSS-6.0.1).
>
> Regards,
> Mahmut
>
>
>> 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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