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

Nathan S. Haigh n.haigh at sheffield.ac.uk
Mon Oct 23 17:37:13 UTC 2006

Sendu Bala wrote:
> Chris Fields wrote:
>> ...
>>> 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.
>> I don't think forcing is necessary, so a CPAN installation shouldn't force
>> someone to install optional modules.  Graph.pm, for instance has a few
>> optional modules, and the tests which use those get skipped and pass so the
>> installation proceeds w/o problems.  We could do the same (any tests using
>> those optional modules display the reason why they are skipped).  
> I should clarify and say that that's what happens in Bioperl as well. 
> The 'forcing' that I talk about is simply what I assume will happen if 
> the user has CPAN set to automatically install dependencies. The user 
> could say 'no' to every question regarding the installation of 
> dependencies that CPAN discovers and Bioperl would still install fine.
> So really the difference between the current situation and, say, the 
> situation when 1.5.1 was released, is that the CPAN user doesn't have to 
> use Bundle::BioPerl for full functionality anymore, but can still chose 
> not to install all the optional external modules.

Obviously, we could maintain a Bundle::BioPerl which includes all
dependencies required for a fully functional Bioperl. I think the whole
idea for a Bundle is to provide a common environment for a particular
package. If for example, someone chooses not to install the dependencies
through CPAN (in the current setup), that can easily go back and install
Bundle::BioPerl and it would retrieve any missing dependencies for a
fully functional Bioperl-core.


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