Add '--color=never' to 'ls' command to repress output with escaped string for color terminal.
Fix the issue of versioncheck.install_ucsc_tools(), add checking of no library installed.
Merge pull request #147 from ny-shao/master

Add '--color=never' to 'ls' command to repress output with escaped strin...
Fix all color 'ls' output issues in make_copy().
Merge pull request #149 from ny-shao/master

Fix all color 'ls' output issues in make_copy().
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