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

Chris Fields cjfields at uiuc.edu
Tue Sep 19 14:50:52 EDT 2006


> Chris Fields wrote:
> > I think any dependencies are supposed to be listed in the Makefile and
> > DEPENDENCIES regardless of how many times they are used or if the method
> is
> > optional.
> 
> Well, the issue here is that doing that would create a circular
> dependency; Ensembl Perl API requires Bioperl. Do the various ways of
> installing Bioperl not 'care' about circular dependencies?

Well, if there are circular dependencies that's a whole different ballgame.
That's what I get for not reading the subject line!  

Could the module be added to bioperl-ext or bioperl-run?  That would break
the circular dependency since the Ensembl API doesn't require those; at
least I think it doesn't.

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



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