Ensure local install works if not user writeable. Install gawk used in tool builds
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Generalize snpEff config regular expression to avoid missing substitution on different sed implementations
Expose documentation as a top level configurable option to include in bcbio-nextgen pipelines
Provide builds for variant calling and prep tools from Marth lab: vcflib, bamtools, ogap
Include cutadapt trimmer
Proteomics: Rework protk installation for new ruby gem install approach. Allow install from either rubygems or source.
Proteomics: Add searchgui and peptideshaker install to bio_proteomics.
Fix for XVFB.
Proteomics: Fixes for many proteomics package installs.