Fix typo in checking for third party tool installation with locally updated LD_LIBRARY_PATH. Fixes chapmanb/bcbio-nextgen#73
Provide fixes for tricky sudo cases: download UCSC tools in temp directory and copy over. Fixes chapmanb/bcbio-nextgen#74 Copy installed binaries instead of move to avoid local permissions issues
Use copy to samtools installation to avoid issues where sudo has no write access to tmpdir
Include missing put command for non-local cloudbiolinux installations. Thanks to Zhi-Wei Lu
Proteomics: Rev target version tint_proteomics_scripts for Galaxy-P.
Refactor Galaxy tool install stuff slightly to reduce cyclomatic complexity and add some code documentation.
Galaxy: Add improved alert message when a Galaxy application fails to install.
Simplify the configuration of CloudBioLinux by determining distribution and dist_name automatically by default when targetting Ubuntu or CentOS.
Merge pull request #81 from jmchilton/master

End need to specify or change distribution and dist_name in most cases.
Add automatic distribution checks for debian, scientific linux and mac os x. #81
Proteomics: Remove problematic ia32-libs package, seems to conflict with gnuplot dependencies. Need to be more specific with 386 libs to install I guess.
Implement auto dist_name check for debian systems.
PEP-8 whitespace fixes and fill out comment on _setup_distribution_environment slightly.
Deployer: Stop targetting custom version of fabric hacked for large file transfers.
Use custom.shared's hack for supporting quiet more heavily. Fixs support for fabric 1.4 (still default on Ubuntu LTS for instance).
Detect Redhat with new distribution autodetection, using centos RPM setup.
Ensure installations create a bin directory to avoid issues when it doesn't previously exist. Fixes chapmanb/bcbio-nextgen#74
Deployer: Bug fix for the non-novm use case, was checking for failed import on incorrect thing.
Deployer: When using novm pseudo provider, if hostname is not set default it to localhost.
Refactor much of the special logic for CloudMan and GalaxyVmLauncher out of core of deployer framework and into a new plugin structure. Though less straight-forward, I think this new structure is more extensible and cleaner.