Deployer: Bug fix for the non-novm use case, was checking for failed import on incorrect thing.
Deployer: Bug fix for novm pseudo provider when hostname is set, default 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.
Galaxy: Allow expansion __contrib_dir__ when looking for Galaxy tools file (galaxy_tool_conf).
Proteomics: Add deployer settings file sample for Galaxy-P (copy this to deploy directory to install Galaxy-P).
Galaxy: Hack to support is_local python venv Galaxy installs.
Galaxy: Enable Brad's cool direct installation process (is_local, no ssh) to work for Galaxy tool dependency installs.
Proteoimcs: Simplify Galaxy-P tools install, just have one file like identical vanilla Galaxy variant, not sure why I ever thought adding seperate proteomics_tools custom install was a good idea.
Proteomics: Initial work on bringing NGS tools into Galaxy-P for RNA-seq driven protein database creation.
Add -r flag to cp in recently (224b7a42ce8cec37e5c7fa2d53879cb7a61af683) updated _make_copy function (was not required with mv). Without this install_omssa for instance in bio_proteomics does not work.
cp --parents does not appear to be doing what we thought it would (error message below)? Placing this mkdir instead seems to fix the problem.

  [localhost] local: sudo bash -c "cp --parents --recursive trinityrnaseq_r2012-10-05 /opt/galaxy/tools/trinity/r2012-10-05"
  cp: with --parents, the destination must be a directory
Galaxy: Improved support in bio_nextgen for Galaxy tool installs of tophat2 and bowtie2.
Galaxy: Change behavior of Galaxy tool installs so all installs are attempted and any errors and exceptions are reported and thrown at the end of the process. I am not sure why one would want to disable this, but the old behavior can be restored by setting galaxy_tool_defer_errors to False. Should we just simplify logic and disable this option?