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

[Sendu Bala]

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.

lib (or at least one entry in your PERL5LIB) needs to point to the 
directory that contains the Bio directory. So:

use lib "strawberry/per/lib C:/strawberry/perl/site/lib/";

Now it will be able to locate Bio::Tools::Hmm. You'll still get your 
original error because you don't have Hmmer installed. See Mark's reply.