[Bioperl-l] [Fwd: Re: Bundle::BioPerl]

Nathan S. Haigh n.haigh at sheffield.ac.uk
Tue Oct 17 12:10:15 EDT 2006


FYI on Bundle::BioPerl

Nathan

-------- Original Message --------
Subject: 	Re: Bundle::BioPerl
Date: 	Tue, 17 Oct 2006 11:52:00 -0400
From: 	Chris Dagdigian <dag at sonsorol.org>
To: 	Nathan S. Haigh <n.haigh at sheffield.ac.uk>
References: 	<45348FB8.4050009 at sheffield.ac.uk>



Hi Nathan,

I've updated the Bundle and uploaded it to CPAN.

I *think* the rationale for keeping it still exists but I'm removed  
enough from Bioperl now that I'll defer to others on the decision.

The basic idea was that BioPerl has a heck of a lot of dependencies  
that it requires of (other perl modules) in order to get all the  
functionality out of it. Many of these dependencies may not be  
present in default Perl installations.  Tracking down all of the  
dependencies and installing them (along with all of the dependencies- 
of-the-dependencies) by hand is a massive pain.

The nice thing about the Bundle is that it lists the core module  
dependencies and it works great with the CPAN.pm module to automate  
the downloading and installation of everything that BioPerl requires.  
The CPAN module is smart enough that when processing *our* bundle it  
will also track down and install anything that our bundle entries  
themselves list as a dependency.

So for unix/Linux systems the Bundle is a great one-liner ("perl - 
MCPAN -e 'install Bundle::BioPerl'" )  way to auto-install or update  
the many perl modules that BioPerl makes use of.

On the windows side, not sure if it is of any help though.

Regards,
Chris




On Oct 17, 2006, at 4:09 AM, Nathan S. Haigh wrote:

> Hi Chris
>
> I've been working on making a PPD for the upcoming Bioperl 1.5.2  
> release. During this time I also updated Bundle::BioPerl to include  
> up-to-date prereqs. I was wondering if you could update the CPAN  
> package? The updated BioPerl.pm file is attached.
>
> There is some talk about why and if we need Bundle::BioPerl  
> anymore. What was the rationale for having it in the first place,  
> and does it still hold true now?
>
> Cheers
> Nath
>


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