[Bioperl-l] [Gmod-gbrowse] Bioperl 1.6 and Bio::Graphics

Lincoln Stein lincoln.stein at gmail.com
Tue Dec 2 11:51:39 EST 2008

Hi Chris,

I am supportive of splitting out Bio::Graphics, but not the Bio::DB::*
modules before the 1.6 release. The only dependency issue is the module
Bio::Graphics::FeatureBase, which is a lightweight hash-based
Bio::SeqFeatureI module that is shared between Bio::Graphics::Feature and
Bio::DB::SeqFeature. It should be renamed and kept in the main bioperl

Will it confuse people if I rename this module Bio::SeqFeature::Lite?


On Wed, Nov 26, 2008 at 3:25 PM, Chris Fields <cjfields at illinois.edu> wrote:

> On Nov 26, 2008, at 12:37 PM, Scott Cain wrote:
>  Hi Chris,
>> While the decision ultimately rests with Lincoln (as, presumably, will
>> most of the work :-)  I'm not sure I agree that the split needs to
>> happen before the 1.6 release.  Consider the case where GBrowse 1.70
>> requires a newer version of Bio::Graphics than is available in
>> BioPerl.  We would put a version requirement in the Makefile.PL for
>> Bio::Graphics::Panel to be some number greater than the current
>> BioPerl release and put it on cpan.  Users would then do the cpan
>> shell shuffle, and get the right version of Bio::Graphics, and if they
>> don't already have BioPerl, they'll get that too (with an older
>> version of Bio::Graphics that will be immediately overwritten).  Is
>> there a flaw (or horrible user experience) in my thinking?
>> Scott
> Sorry Scott, forgot to mention it wouldn't just be Bio::Graphics.  Lincoln
> also mentioned Bio::DB::GFF and Bio::DB::SeqFeature::Store (basically
> anything Gbrowse-related) would be included, so maybe bio-gbrowse or similar
> would be a better name.
> If you like we could postpone a split (less work for the release).  A split
> bio-gbrowse release would just overwrite the older modules as you mention.
>  However, I plan on having regular point releases to CPAN; how do we want to
> handle Gbrowse-related bug fixes in a point release down the road, after a
> Bio::Graphics split?
> Do we stop Bio::Graphics fixes at a certain point after a post-1.6 split so
> an installation script always finds the latest Bio::Graphics::Panel?  Or do
> we want to merge those fixes into the point release regardless, just in
> case?
> chris
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Lincoln D. Stein

Ontario Institute for Cancer Research
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Cold Spring Harbor Laboratory
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