[Bioperl-l] Problems with Bioperl-ext package on WinVista?

[Chris Fields]

Bio::Tools::Hmm doesn't use HMMER, it uses a C-based extension in  
bioperl-ext that generates HMM's (XS-based bindings I think).  I have  
managed to compile it successfully on Ubuntu and Mac OS X, but  
WinVista is a whole different bag-o-worms altogether (untested AFAIK).

For the record, I do not recommend using it; I'm unsure about it's  
maintenance status, so it may be released separately.  It would be  
best to use something better supported, such as the HMMER wrapper in  
bioperl-run and the hmmer parsers in bioperl-core.  We may also have  
wrappers for similar code available in biolib at some future point.

chris

On Aug 11, 2009, at 1:52 PM, Jonny Dalzell wrote:

>
> Hi,
>
> I'm as sure as I can be.  I look in the HHMER folder and it contains
> "Domain.pm", "Results.pm", and "Set.pm".  I thought perhaps it was  
> something
> to do with @INC, but I put
> "use lib "strawberry/per/lib C:/strawberry/perl/site/lib/Bio/ 
> Tools/";" at
> the top of my script, which definately encompasses the directory it  
> should
> be in, and I still get...
>
> "Can't locate Bio/Tools/HMM.pm in @INC (@INC contains: strawberry/ 
> per/lib
> C:/strawberry/perl/site/lib/
> Bio/Tools/ C:/strawberry/perl/lib C:/strawberry/perl/site/lib .) at  
> HMM.txt
> line 5.
> BEGIN failed--compilation aborted at HMM.txt line 5."
>
> I'm out of ideas.
>
> Jonny
> -- 
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>
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