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

Mark A. Jensen maj at fortinbras.us
Tue Feb 9 22:56:36 EST 2010


( btw, je ne savvy pas: that should be Bio::DB::Sam (in the Bio-SamTools 
distribution) -- ugh MAJ)
----- Original Message ----- 
From: "Mark A. Jensen" <maj at fortinbras.us>
To: "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 4:21 PM
Subject: Re: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?


> 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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>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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>>
>>
>
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