Hi, it would be nice to Bundle::Bioperl package which should wrap all the modules optional for bioperl. Please cross-talk with sci herd, namely ribosome@gentoo.org. See thread named "[Bioperl-l] Optional 'circular dependency' ok?" in bioperl-l mailing list archives currently discussed. M.
The Bundle::Bioperl is probably not well maintained anymore, maybe think of hardcoding deps as listed here: http://bio.perl.org/wiki/BioPerl_Dependencies http://bio.perl.org/wiki/Installing_Bioperl_for_Unix
Equivalent functionality supplied by sci-biology/bioperl[minimal].