Try the following uber 1337 commands (based on this):
mv ~/perl5 ~/notperl5
wget -O - http://cpanmin.us | perl - -L ~/perl5 --self-upgrade local::lib
OK, now add your ~/perl5 dir into git...
cd ~/perl5/ ; git init ; git add . ; git commit -m 'initial import'
This will help you keep things in order over time.
You can then use git to see exactly what you did, and commit if it worked OK. i.e.
git add . ; git commit -m 'BioPerl and Bio::DB::Sam installed'
(Once you have confirmed that it's working.)
Once your local::lib is in git, you can do lots of stuff like if something is breaking, just edit it in there to insert debugging or whatever and then just reset --hard to get rid of it after you figure out what is going on, etc.
Thanks to rbuels on irc://irc.freenode.net/#bioperl for helping with this!
(All the above is his doing).