[Bioperl-l] Optional 'circular dependency' ok?

Chris Fields cjfields at uiuc.edu
Wed Sep 20 14:55:11 EDT 2006


My point was, is there any way we can have two sets of modules: one set that
is 'required', and another that is 'optional' (for additional functionality,
but not installed)?  And have Makefile.PL test for all of them?  

If we can have both, Sendu could have the Ensembl API be 'optional' (not
installed by default) but checked upon installation.  There are a few others
'dependencies' which are critical for only one or two modules that could
also be considered optional, such as Ace, Convert::Binary::C,
Spreadsheet::ParseExcel, Bio::ASN1::EntrezGene, etc.

If it's too much of a pain to worry about we can just have Sendu designate
the Ensembl requirement in the POD like he suggests. 

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: Mauricio Herrera Cuadra [mailto:arareko at campus.iztacala.unam.mx]
> Sent: Wednesday, September 20, 2006 1:25 PM
> To: Hilmar Lapp
> Cc: Chris Fields; 'Sendu Bala'; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Optional 'circular dependency' ok?
> 
> Hilmar Lapp wrote:
> > On Sep 20, 2006, at 12:06 PM, Chris Fields wrote:
> >
> >> The Makefile.PL doesn't require that the dependencies are installed
> >> if using
> >> 'perl Makefile.PL',
> >
> > Right, I know. However, package maintainers may use this information
> > to decide what to include in their pre-packaged dependencies and what
> > not to.
> >
> 
> Yeah, that's precisely how I track dependecies for the BioPerl FreeBSD
> ports.
> 
> Mauricio.
> 
> --
> MAURICIO HERRERA CUADRA
> arareko at campus.iztacala.unam.mx
> Laboratorio de Genética
> Unidad de Morfofisiología y Función
> Facultad de Estudios Superiores Iztacala, UNAM




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