Snpeff: fix version number.

Closes #700.
libsequence: add gsl dependency

Closes #694.
pymol: add test
Added Formula for the NeXus file format.

Closes #689.
velvet: rm trailing whitespace
snpeff: Correct the database directory in caveats

The databases will be installed in #{share}/java/data
was
The databases will be installed in ~/snpEff/data
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.
Vips: make core deps recommended

libvips has a lot of dependencies: some are used to implement core
functions, some are used to add support for less-used file formats.
Previously all non-required dependencies were :optional, so, by default,
libvips was missing a lot of features.

This patch tags dependencies which are used to implement vips operations
and support for common file formats as :recommended and leaves those
which are used for less-common file formats as :optional.

Closes #707.
Scalapack: add head.
Mumps: select compiler based on :mpi.
Ipopt: Upgrade to 3.11.7 and build fixes.

- Remove MPI compilers from environment as they crash the linker
- Apply patch if Mumps was built in parallel
- Add option to skip build-time tests.

Closes #656.
Catch up with upstream audit changes