Proteomics: Old EMBOSS download used by Galaxy-P no longer available, update to 6.6.0. (This probably needs to be updated other places as well).
Proteomics: ms2preproc disappeared from other site. Found a new download. Small updates to install procedure.
Fill in some missing gaps between Ubuntu and CentOS/SL (base R). Add documentation pointer to fill in some more manually (rpy and scipy).
Update libraries.py to use env.safe_ functions.
Fixes to yum packages to address issue 84 reported by @andersje.
Eliminate missing yum dependencies boost141/boost141-devel. boost-1.41 is now the default.
Small bug fixes.
Adapt CloudBioLinux deployer to enable Galaxy tool shed client to easily install tools configured in CloudBioLinux.

@chapmanb had this idea at the BOSC 2013 CodeFest. I thought it was a bit ambitious and heavy at the time, but the deployer + local install stuff make it really easy to do one off CloudBioLinux tool installations (Galaxy or otherwise).

Galaxy tool shed client stuff is working and I will submitted to the Galxy project via pull request shortly. Basically, package definitions in tool_dependencies.xml support a new action type with 4 optional attributes.

  <action type="cloudbiolinux_install"
                [cbl_revision="<revision to checkout(default=master)>"]
                [cbl_url="<cbl_repo_url(default=https://github.com/chapmanb/cloudbiolinux)>"]
                [tool_name="<tool_name(default=use dependency package name)>"]
                [tool_version="<tool_version(default=use dependency package version)>"]
          />

The test_install_galaxy_tool.py script demos/tests roughly what the tool shed client does (though without Galaxy).
Partial work on CentOS 6.4 compatibility of builds: use installed anaconda python, avoid GCC overrides from older CentOS versions. Update download for cortex_var. Fixes #85. Fixes #86