[Bioperl-l] bioperl / emboss on windows

[uludag at ebi.ac.uk]

> 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");