Upgraded Tophat to 2.0.10.
Added VectorBase downloader and two mosquito genomes.
Latest bcbio.variation release. Fixes chapmanb/bcbio-nextgen#194
Add homebrew versions of vcflib and glia packages, and make available to bcbio-nextgen installer. chapmanb/bcbio-nextgen#204
Add a biopython flavor that installs biopython plus dependencies into an isolated ~/biopython directory. For testing/installing Biopython: @tiagoantao
Drop fastx_toolkit requirement for bcbio-nextgen install
Added non-s3 hosted biodata install instruction.
Update to latest version of Broad GATK bundle and dbSNP. Thanks to Severine Catreux
Install latest bcftools and samtools release candididates as part of bcbio-nextgen pipeline, avoiding samtools conflicts with homebrew-science
Add symbolic link to .fa file from bowtie2 directory.
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Added patch to fix Tophat 2.0.10 not working with samtools 0.2.0.

When it gets fixed upstream, this should be removed.
Avoid unlink errors with samtools if not currently present. Fixes chapmanb/bcbio-nextgen#219
Pin bedtools to previous version to avoid build errors on 2.18.0 (arq5x/bedtools2#3). chapmanb/bcbio-nextgen#220 chapmanb/bcbio-nextgen#219
Revert to samtools 0.1.19, installing version without conflicting bcftools. Fixes chapmanb/bcbio-nextgen#221
Ensure tabix installed to provide bgzip without samtools 0.2.0
Roll back Tophat to 2.0.9-- there are some continuing issues with 2.0.10.
Remove bedtools version restriction. Released 2.18.1 now builds cleanly
Improved handling of previous version installations. Cleans up after old version installation to prevent phantom untracked changes. Provide untap/tap fix if initial update fails due to local changes
Move to latest version of freebayes