[Bioperl-l] Bundle::BioPerl and Pre-reqs

Nathan S. Haigh n.haigh at sheffield.ac.uk
Mon Oct 23 16:38:00 UTC 2006

Sendu Bala wrote:
> Chris Fields wrote:
> [option 1]
>>> Oh, so this effectively means that our 'optional' dependencies are 
>>> installed for CPAN users, which matches up to my 'force the
>>> optional ones anyway' desire, leaving Bundle::BioPerl without any
>>> use.
> [option 2]
>>> Makefile.PL could be altered again to remove from PREREQ_PM those 
>>> modules the user didn't already have installed, thus CPAN would
>>> only install Bioperl itself and nothing optional. The user could
>>> then install Bundle::BioPerl if they wanted a quick way of getting
>>> all the optional stuff to work.
>>> I'm happy either way; what do other people think?
>> I think that we should have it so Bioperl installs as-is (no
>> additional reqs) and have Bundle::BioPerl used as a convenient way to
>> install all optional modules for full functionality.
> Note we're specifically considering a CPAN install here. If you download
> the tar.gz or use cvs, [option 1] doesn't affect you. Bundle::Bioperl is
> still needed as a convenience if you want to install the optional
> external dependencies.
>> The catch is to make sure that any optional installations do not
>> crash tests during a CPAN bioperl installation, otherwise they aren't
>> considered optional by CPAN, and the install won't work without
>> forcing it.
> I'm pretty sure this isn't a problem, though it would be nice if someone 
> could test it on a clean system: does 'make test' pass all ok with none 
> of the optional modules installed?

I could definitely do this on WinXP and *possibly* on a Linux system.

> Anyway, to reiterate the question: Do we care if CPAN users get all the 
> optional external dependencies installed for them automatically, or do 
> we want to force them to install Bundle?

I'd prefer any dependencies, whether the are seen as vital to the main
functionality of Bioperl or not actually specified in PREREQ_PM (as they
currently are). A dependency is a dependency - is it not? If a
distinction is to be made based on whether the requiring module is
simply adding additional functionality to Bioperl-core, then shouldn't
it be moved out of core and into another package as with the run modules
if we are to have "optional" dependencies?

my 2p

> The current situation is: CPAN users will get all optional external 
> dependencies without using Bundle::BioPerl. Manual installers of bioperl 
> (from tar.gz, from cvs etc.) must install Bundle::BioPerl manually to 
> get full functionality.
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