maker: Depend on Bio::Perl

Depend on Bio::Perl rather than Bundle::BioPerl. The former installs
BioPerl (CJFIELDS/BioPerl-1.6.922.tar.gz), the latter installs the
dependencies of BioPerl (CRAFFI/Bundle-BioPerl-2.1.8.tar.gz).
viennarna: use test block

Test output with assertion.
root 5.34.17

Closes #702.
root: add --with-qt option

Added option to enable (or, by default, disable) Qt graphics
backend and GSI's Qt integration.

Closes #678.
cdo 1.6.3

Closes #703
bwa 0.7.7

Add simple test.
Velvet make updated

make arguments now handled through options, not environmental variables.

Closes #706.
update vips.rb to latest stable

also improve support for building against graphicsmagick, see:

https://github.com/jcupitt/ruby-vips/issues/50

Closes #705.
Maxima 5.32.1

Closes #701.