I installed bioperl using this script. It'll do a fresh install of everything needed for bioperl, but it is "forced", so it will take some time...
#!/usr/bin/perl
use strict;
use warnings;
use CPAN;
CPAN::Shell->force('install',
"Bundle::BioPerl",
"Bio::Seq",
"Bio::SeqIO::staden::read",
"Bio::Factory::EMBOSS",
"Bio::Tk::SeqCanvas",
"Bio::DB::Annotation");