Avoid use of brew versions, which has been deprecated. Improve version detection and avoid issues with missing brew components. Fixes #151. Fixes #152
Avoid error when samtools keg missing and we check for bcftools. Fixes #153
Add AlienTrimmer to the bio_nextgen custom installer.
Latest FreeBayes version: 0.9.13
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Ensure htslib is updated prior to bcftools installation to avoid version conflicts. chapmanb/bcbio-nextgen#301
Update the list to packages to be explicitly removed during cloud image cleanup
Update STAR to 2.3.1z.

.1z has the ability to add read groups while aligning, which
saves a step getting final BAM files ready for GATK.

Usage: --outSAMattrRG ID:xxx CN:yy "DS:z z z
Force removal of htslib prior to upgrade to avoid depedency issues from having multiple versions installed
Move FreeBayes build to use brew recipe. Add Platypus caller
Include vt variant manipulation tool in standard build for bcbio-nextgen
Fix platypus brew target to avoid naming collision
Update to Ensembl release 74.

Also remove the unnecessary FASTA file that is generated from
the final tarball.
Update to latest releases of RNA-seq data with Ensembl 74 annotations
Update to latest releases of RNA-seq data with Ensembl 74 annotations
Add featureCounts.

This will replace htseq-count; it has similar functionality and
is about 10x faster.
Do full cleanup of outdated brew package prior to reinstall. Avoids unexpected state errors when upgrading.
Fix typo in ipython config file template
Add AlienTrimmer and featureCounts to minimal flavor.
Workaround for bowtie 2.2.0 not working with Tophat.

'Note: the latest version of Bowtie2 (v2.2.0) is not compatible with TopHat2.
We will fix this issue soon.'

So for now go back to installing from source so we can use the 2.1.0 version
which works.