[Bioperl-l] Smaller Bioperl Modules

Chris Fields cjfields at uiuc.edu
Mon Jul 21 22:39:34 EDT 2008

Hi Nat!

We have discussed breaking things up but there was never a full  
consensus on it and I think, in the long run, it would have been too  
hard to convince everyone, particularly the CPAN folk, that it made  
sense to have tons of separately installable mini-bioperl modules.

We do still intend on paring down core to the bare essentials,  
removing as many dependencies as possible, and having a separate tools  
and dev set of modules.  I added a page on the wiki on my proposal for  
the intended split (others have added a few things here and there):


It's worth reviving this discussion again; when I have more time I  
want to spearhead a 1.6 release.


On Jul 21, 2008, at 6:09 PM, <Nathan.Watson-Haigh at csiro.au> wrote:

> Hi all,
> I'm developing a web-based application and it'd be cool to use some
> Bioperl modules. However, I'll be providing my tool for downloaded and
> installation on a web server, so having to ask the sys admin to  
> install
> all of bioperl where I only need a few modules is overkill and is  
> likely
> to cause installation headaches.
> Since I've been out of the loop for quite a while now, I was wondering
> if any decisions had been made about whether or not Bioperl was  
> going to
> be released on CPAN in smaller sets of modules with correct  
> dependencies
> and possibly a Bundle::Bioperl? It'd be nice to have my application,  
> for
> example, depend on Bio::SeqIO, such that only Bio::SeqIO::* and it's
> dependencies are installable through CPAN.
> Cheers,
> Nath
> -------------------------------------------------------------
> Dr. Nathan S. Watson-Haigh        (publish under Haigh, N.S.)
> OCE Post Doctoral Fellow
> CSIRO Livestock Industries
> J M Rendel Laboratory
> Rockhampton
> QLD 4701                              Tel: +61 (0)7 4923 8121
> Australia                             Fax: +61 (0)7 4923 8222
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign

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