genometools: Add head and DOI
bedtools: Add DOI
samtools: add vcfutils.pl to without-bcftools

vcfutils.pl is now included in the latest bcftools release candidate
(rc8) so conflicts when installed alongside samtools. This removes the
conflict when passing --without-bcftools. chapmanb/bcbio-nextgen#426

Closes #910.
root: patch not required with HEAD

Patch is only required for non-HEAD users at or before 5.34.18
without XCode installed.

Closes #905.
spatialite-gis: fix compilation with wxWidgets 3

See also https://github.com/Homebrew/homebrew/commit/b31227d6ef602142ea399b04211d306eaaea674c

Closes #298.
Closes #456.
galib: fix clang error with undeclared identifiers

Closes #908.
mummer: Add DOI
netcdf: patch to fix hdf5 1.8.13 missing symbols

HDF5 1.8.13 removes symbols related to MPI POSIX VFD, leading to
errors when linking hdf5 and netcdf5 such as "undefined reference to
`_H5Pset_fapl_mpiposix’".

The patch has already been added to netcdf, and will be included
in the next release.

Fixes #911.
Closes #916.
armadillo 4.300.3

Copy examples/ directory to prefix.

Closes #912.
bali-phy: switch to needs :cxx11

Closes #925.
bali-phy 2.3.4

Closes #922.
root: tabs -> spaces
ensembl-tools: update shasum, add head
therion 5.3.15

Closes #924.
htslib: Remove razf

razf has been removed in HEAD. See
https://github.com/samtools/htslib/pull/74
htslib: Conflicts with tabix

Both htslib and tabix install bin/tabix
htslib: Add a test
samtools: Do not build razip

razip has been removed upstream. See
https://github.com/samtools/htslib/pull/74
samtools: Fix a typo. Htslib should be htslib
samtools: 0.2.0-rc8 devel