Created install_GSC_patches on vcr.py and modified custom.yaml to accept it.
Merge branch 'master' of github.com:JCVI-Cloud/cloudbiolinux
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
Updating vcr.py for latest VIGOR tarball
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.
Support galaxy rsync indexes contained in subdirectories, like microbes. Thanks to @brainstorm
Remove GATK queue build
Update to latest version of picard
Do not attempt to install condor on Ubuntu 12.04 LTS, it is not available.
Merge pull request #68 from jmchilton/master

Do not attempt to install condor on 12.04 LTS.
Provide a more flexible way to determine pip executable. Thanks to Tim Fennell
Check for TMPDIR on systems where missing environmental varialbles cause errors. Thanks to Tim Fennell