[Bioperl-l] BioPerl CPAN

[Aaron J Mackey]

Unfortunately, all of this proposed effort boils down to simply splitting
up the monolithic Bioperl distribution into lots of mini distributions
(potentially with different CPAN authors).  There are already other
modules/distributions in the Bio:: namespace (BioPerl does not have
exclusive rights to that namespace).

I would argue that if, for example, I'd like to create a set of modules
that calculates codon bias 15 different ways
(Bio::Analysis::Protein::CodonBias, and associated "engines"
Bio::Analysis::Protein::CodonBias::CAI,
Bio::Analysis::Protein::CodonBias::T2, etc), that I should be able to
upload Bio-Analysis-Protein-CodonBias-1-01.tar.gz to CPAN by myself,
without requiring a new BioPerl release.  That's a good thing.  And
perhaps my Bio::A::P::CodonBias module actually uses the BioPerl core
Bio::SeqIO and other modules to do it's job.  Or maybe it doesn't.
There's no contract that says all the Bio::* modules have to work together
(in fact, they already don't).  Not all the CGI::* modules work together,
not all Net::* modules work together, etc etc.

So maybe instead of worrying about what BioPAN or BPAN or whatever is, we
start thinking about what bits are actually "core library" and what bits
are "application".  And then asking ourselves what does splitting up our
current core into lots of tiny bits get us (besides possibly more rapid
release schedules for each tiny bit).

-Aaron


On Tue, 1 Jul 2003, Jarkko Hietaniemi wrote:

> > 1. Where can be get more information how CPAN/PAUSE works?
> >
> > http://www.cpan.org/modules/04pause.html gives some guidelines but not
> > enough.
> >
> > Are there any written guides to the whole system which are essential
> > reading?
>
> Ummm, what kind of information do you mean?  The CPAN author and
> maintenance menus are pretty self-explanatory.  There is some very
> light technical background material on PAUSE/CPAN in
> http://www.cpan.org/misc/ZCAN.html but that is irrelevant for the
> module/author maintenance.
>
> The 'bioperl CPAN admin' should probably be someone with some CPAN
> uploading experience under their belt, of course...
>
> > 2. Jarkko, how do we make sure that the new effort does not conflict
> > with the current bioperl bundle in CPAN? We will be using the same Bio
> > name space, aren't we?
>
> I don't know whether you will be using the same name space, but as far
> as I know one _can_ upload modules with conflicting names.  There will
> be warnings, of course, but I don't remember exactly to whom.
>
> > 3. How do we split up the current bioperl-live?
>
> Pass. :-)
>
>

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey at virginia.edu