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

[Mark A. Jensen]

Jonny,
It will run in Win/Vis but there are some caveats. The BioPerl package has some 
plain C components, as Rob pointed out. These need to be compiled, and the 
objects/libraries put in the right place. CPAN will cause this to happen when 
you have a compiler available; ActiveState .ppm will download the binaries 
directly from the repository (my understanding, anyway). CPAN is always 
available by doing

> perl -MCPAN -e shell

but you may not have a C compiler around. This is a little tricky. You can 
either explore Visual C/C++ options from MS here 
http://msdn.microsoft.com/en-us/library/ms950410.aspx, or you can do as I do, 
and install Cygwin (www.cygwin.com), which creates a linux-like environment with 
GNU compiler tools and many other (wonderful, IMHO) goodies. Not as wonderful as 
the real thing, I grant. Which bring me to a third possibility, that I haven't 
tried, which is an Ubuntu box running in a VM under Windows, or as a dual-boot 
system (https://help.ubuntu.com/community/WindowsDualBoot).
MAJ
----- Original Message ----- 
From: "Jonny Dalzell" <jdalzell03 at qub.ac.uk>
To: <Bioperl-l at lists.open-bio.org>
Sent: Tuesday, August 11, 2009 4:29 PM
Subject: Re: [Bioperl-l] Problems with Bioperl-ext package on WinVista?


>
> Hi,
>
> thanks.  I did install HHMER from the site Mark suggested, and it is within
> the directories that perl recognizes when reading the script...still I get
>
> "The C-compiled engine for Hidden Markov Model (HMM) has not been installed.
> Please read the install the bioperl-ext package"
>
> Is it possible that this module simply won't run through windows?
>
> jonny
>
>
>
> Sendu Bala-2 wrote:
>>
>> 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.
>>
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>>
>>
>
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