[Bioperl-l] Test overhaul complete

Sendu Bala bix at sendu.me.uk
Wed Jun 27 16:22:13 EDT 2007

Nathan S. Haigh wrote:
> It seems (to me at least) that Bioperl modules could/should? be released
> as individual modules and that "bioperl" would really constitute a
> "bundle" of all these modules - in terms of CPAN anyway. Am I correct in
> this thinking? The Bio::ASN1::EntrezGene could simply require a
> particular module rather than the whole of bioperl - might get out of
> the circular dependency theoretically!?

No, it wouldn't. The 'problem' only arises because the user is 
/choosing/ to install both Bioperl and Bio::ASN1::EntrezGene at the same 
time. So even if Bioperl was released as separate modules there would 
still be that 'bundle' and users would still choose to do the same 
thing: install all the Bioperl modules as well as all its /optional/ 
recommended modules. And there lies the problem: Bio::ASN1::EntrezGene 
requires  Bioperl modules, and one Bioperl module requires 
Bio::ASN1::EntrezGene, so the circularity isn't solved.

Bio::ASN1::EntrezGene requires Bio::Index::AbstractSeq
Bio::Index::AbstractSeq requires a couple of Bioperl modules, including 

Bio::SeqIO::entrezgene requires Bio::ASN1::EntrezGene and a bunch of 
Bioperl modules, including Bio::Root::Root.

You only avoid circularity by choosing not to install everything in one 
go. Which is something you can do right now with no problems.

More information about the Bioperl-l mailing list