[Bioperl-l] Withdraw Bio::Graphics and Bio::DB::SeqFeature from bioperl distribution?
cjfields at illinois.edu
Mon Nov 10 22:58:44 EST 2008
On Nov 10, 2008, at 4:57 PM, Lincoln Stein wrote:
> Hi Folks,
> Sorry, I sent my letter out while multitasking, which was
> inappropriate for such a nuanced subject.
> Here's my feeling about the issue, which is very similar to Chris's
> approach: Bioperl should be split up into a core API containing
> Bio::Root, the interface modules, and some of the really basic
> modules such as Bio::SeqIO. There are then a series of separately
> maintained and released modules that build on top of BioPerl and
> using it as a dependency. I am not in favor of having a "separate
> monolithic distribution" however. I'd prefer it to be more like this:
> • Bio::Perl -- the core distribution, containing Bio::Root,
> Bio::Seq, BioSeqFeature, Bio::SeqIO and Bio::Annotation
> • Bio::Align -- alignment support
> • Bio::Ontology -- ontology support
> • Bio::Microarray -- microarray support
> • Bio::PopGen -- population genetics
> • Bio::SeqEvolution -- evolutionary biology
> • Bio::Structure -- structures
> • Bio::Tree -- trees
> I wonder how many interdependencies there are to disentangle?
> In the immediate future, it'd be great to get the regression tests
> working 100% and do a CPAN release, but this may be easier said than
BTW, I would like to add to that list Bio::Tools (Bio::Tools* related
changes suggested recently by Heikki) and Bio::Dev (for in development
or untested modules, or experimental modules with an unstable API).
I'll work on a few bugs towards getting 1.6 released with a rough
timeline for end of Nov, maybe even Thanksgiving. We can work on
splitting things up after that.
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