[Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?

Mark A. Jensen maj at fortinbras.us
Tue Feb 9 18:30:50 EST 2010


I'm game-- it sounds like the right direction to go-

----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "Robert Buels" <rmb32 at cornell.edu>; "BioPerl List" 
<bioperl-l at lists.open-bio.org>; "Dan Kortschak" <dan.kortschak at adelaide.edu.au>
Sent: Tuesday, February 09, 2010 6:07 PM
Subject: Re: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?


Mark,

If I've learned anything from the 1.6 release series, I would rather it not be 
bound to the bioperl core release cycle, particularly if we are progressing 
towards splitting up bioperl anyway.  In that light it makes more sense (at 
least to me) to move this into either a focused set of modules for next-gen 
analysis, or as focused packages based on the specific functionality (e.g. all 
BowTie modules bundled together, all bioperl-related Samtools bundled together, 
etc).

Bascially, we would set up both you and Dan as co-maintainers, and push all 
related code under the BIOPERLML CPAN mantle as primary maintainer.  This way 
any of the co-maintainers can step in and push out new releases if needed.

chris

On Feb 9, 2010, at 3:21 PM, Mark A. Jensen wrote:

> Yeah, this is getting kinda hairy-- B:T:R:Samtools is
> a basic wrapper for anything that wants to use
> Bio::DB::Samtools ( lstein's samtools library wrapper,
> a CPAN and not a BioPerl module. Savvy?). Because
> its likely that other parser-like modules will want to
> use samtools ( as well as wrapper-like modules), I
> would vote for moving Samtools and Samtools::Config
> into the bioperl-live version of Bio::Tools::Run.
> (A question for another day is, should we/can we
> coalesce the two instances of Bio::Tools:Run,
> and where?)
> MAJ
>
> ----- Original Message ----- From: "Robert Buels" <rmb32 at cornell.edu>
> To: "BioPerl List" <bioperl-l at lists.open-bio.org>; "Dan Kortschak" 
> <dan.kortschak at adelaide.edu.au>
> Sent: Tuesday, February 09, 2010 3:27 PM
> Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?
>
>
>> Bio::Assembly::IO::bowtie uses Bio::Tools::Run::Samtools, which is part of 
>> bioperl-run.  Doesn't that introduce a circular dependency between 
>> bioperl-live and bioperl-run?
>>
>> Perhaps it should be split out into its own CPAN distribution that depends on 
>> both bioperl-run and bioperl-live?  Or maybe some way can be found for it to 
>> not use Bio::Tools::Run::Samtools?
>>
>> Rob
>>
>> -- 
>> Robert Buels
>> Bioinformatics Analyst, Sol Genomics Network
>> Boyce Thompson Institute for Plant Research
>> Tower Rd
>> Ithaca, NY  14853
>> Tel: 503-889-8539
>> rmb32 at cornell.edu
>> http://www.sgn.cornell.edu
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