Add glusterfs-client package under cloudman
brew cleanups: handle  checks on new repositories, chmod additional directories, and install brew man documentation
Bump bcbio.variation to latest release
Enable homebrew/linuxbrew integration as part of default CloudBioLinux installation. Replace custom packages with homebrew equivalents. Update ngs_pipeline_minimal flavor for bcbio-nextgen builds
Ensure env.user passed via CloudBioLinux local deploy calls. Fixes chapmanb/bcbio-nextgen#148
Improve resiliancy of brew installation to partial installs. Correctly check for locally installed brew not in PATH
Install baseline packages required for brew installs. Handles perl libraries not installed by default with cpan minus
Setup perl environmental variables and installs to handle isolated directories: supports lumpy and vcftools perl dependencies
Bump biobambam version and avoid custom novosort included with brew novoalign
Remove homebrew build targets requiring more complicated builds until we get a better handle on directing the gcc to use
Ensure brew test during installation matches that used for installation to avoid missing Homebrew/Linuxbrew errors: #123
Ensure CloudBioLinux environmental variables set for libaries and perl even when install directory is in the current PATH
Ensure ruby installed for bootstrapping homebrew on bare machines during bcbio-nextgen install. Fixes #123
Enables pass through of current on PATH gcc and g++ compilers to brew. Requires Homebrew/linuxbrew#29
Update sambamba to latest version with multicore support. Move to a homebrew recipe and remove older custom script.
Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux