[Bioperl-l] Withdraw Bio::Graphics and Bio::DB::SeqFeature from bioperl distribution?

Lincoln Stein lincoln.stein at gmail.com
Mon Nov 10 18:05:27 EST 2008


I think the problem is that gbrowse is moving very rapidly due to the demand
for a large number of new feature types, primarily in population and
functional genetics. Every time there is a new feature type, I add a new
glyph to Bio::Graphics, and this goes into bioperl-live. So it really makes
sense for Bio::Graphics to have its own release schedule -- it depends only
on Bio::Root and Bio::SeqFeatureI, so the dependencies are minimum.

Alternatively, I could publish a separate package of Bio::Graphics::glyphs
as "add ons", but it would still be hard to make bug fixes to core glyphs.

The issue with Bio::DB::SeqFeature is a little different -- there were a
series of bug fixes last summer, and I'd like them to be in an official
release. This, and Bio::DB::GFF, are pretty stable, I think.


On Mon, Nov 10, 2008 at 5:51 PM, Mark Johnson <johnsonm at gmail.com> wrote:

> On Mon, Nov 10, 2008 at 2:25 PM, Lincoln Stein <lincoln.stein at gmail.com>
> wrote:
> > Hi All,
> >
> > The glacial pace of official bioperl releases is interfering with my
> ability
> > to package GBrowse 2.00 into debian and rpm packages. Is there any
> objection
> > if I withdraw Bio::Graphics and Bio::DB::SeqFeature from the bioperl
> > distribution and turn them into independent CPAN modules?
> How so?  I don't disagree with your characterization of the pace of
> releases, but if 1.5.3 or 1.6 was released tomorrow, would that really
> solve all your problems?
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Lincoln D. Stein

Ontario Institute for Cancer Research
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Toronto, ON, Canada M5G0A3
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Assistant: Stacey Quinn <Stacey.Quinn at oicr.on.ca>

Cold Spring Harbor Laboratory
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(516) 367-8380
Assistant: Sandra Michelsen <michelse at cshl.edu>

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