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.
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
Avoid using pwd which fails on some shells. Inject current system install into path when checking for programs for installation into non-system paths
Flexibly choose between default python and python with extension based on version numbers. Thanks to Tim Fennell
Outline of potential idea for creating virtualenvs for multiversioned Galaxy tools.