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

Chris Fields cjfields at uiuc.edu
Thu Sep 21 09:45:41 EDT 2006


Ah, but would we then have a dependency for Module::Install?  ;>

Kidding, kidding.  We should work out viable options.  If we could lower the
number of 'required' modules w/o wreaking havoc on Makefile.PL, yet allow
testing for 'optional' modules, that would be great.  This is probably
something to think about long term (before v 1.6) vs short term (v. 1.5.2).

As Hilmar stated, though, we may need to have testing for the 'optional'
modules be optional itself.  Maybe have a query for optional module tests
like we do for Bio::DB::GFF tests?

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


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Nathan S. Haigh
> Sent: Thursday, September 21, 2006 2:44 AM
> To: Chris Fields
> Cc: 'Mauricio Herrera Cuadra'; 'Hilmar Lapp'; bioperl-l at bioperl.org;
> 'Sendu Bala'
> Subject: Re: [Bioperl-l] Optional 'circular dependency' ok?
> 
> Chris Fields wrote:
> > 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?
> >
> I've just seen Module::Install that may well do this type of checking of
> dependencies. See
> http://search.cpan.org/~audreyt/Module-Install-
> 0.64/lib/Module/Install.pod#SYNOPSIS
> 
> Might be worth a look?
> Nathan
> > 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
> >
> >
> 
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