Avoid writing to biolinux log which can cause permission issues in local mode depending on /var/log setup
Updates to PeptideShaker and SearchGUI.
Proteomics: Update to peptideshaker/searchgui.
Allow specify custom modules for protftpd compile.
Update freebayes to latest revision with fixes for soft-clipped reads at start of contigs
Remove RVM install from ports on Ubuntu thanks to feedback from @jmchilton
Proteomics: SearchGUI/PeptideShaker enhancements.
Implement new fabricrc option `autoload_galaxy_tools`. This defaults to False, but if True it will cause the sourcing of galaxy env.sh to be placed into `user`'s .bashrc file. This allows galaxy to maintain separate isolated environments, while also letting users easily utilize tools setup for Galaxy from the command-line. This should be considered a highly experimental feature, it has clear problems (potentially loading conflicting virtualenv environments for instance).
libtokyocabinet9 is not available in Ubuntu percise, but libtokyocabinet-dev brings in libtokyocabinet8. So I think a more generic way to get this library is just install the dev package (as done with the following line).
Add R libraries for mass spec analysis, along with required system library (libnetcdf-dev) required by one of these packages. Mostly these libraries are the ones outlined by @ypriverol in this blog post http://www.r-bloggers.com/why-r-for-mass-spectrometrist-and-computational-proteomics/.
Proteomics: Clean up and updates for MZMine, OpenMS, PeptideShaker, SearchGUI, and pride tools.
Proteomics: Work toward building a flavor for combined Galaxy + CLI + Desktop usage modeled after the awesome Current Protocols papers. Adding R & Ruby libraries to galaxyp flavor.
Implement general helper functions laying the groundwork for Chef (http://wiki.opscode.com/display/chef/Home) and Puppet (https://puppetlabs.com/) integration.
Extend CloudBioLinux to allow configuration via Chef recipes.

 - Chef cookbooks may be placed in config/chef/cookbooks.
 - Recipes can be provisioned one at a time from the command line by specifing fabric operation install_chef_recipes, all at once by setting target=chef_recipes, or as part of a full install (default). This mirrors closely 'custom' install operations.
 - Fabric properties are added to Chef's node environment, extra node properties can be added to config/node_extra.json (or flavor variant of this file). chef version of fabric properties are prefixed with cloudbiolinux_.
Extend CloudBioLinux to allow configuration via Puppet classes.

 - Puppet modules may be placed in config/puppet/modules.
 - Puppet classes can be provisioned one at a time from the command line by specifing fabric operation install_puppet_class, all at once by setting target=puppet_classes, or as part of a full install (default). This mirrors closely 'custom' install operations.
 - Fabric properties are added to Puppet's environment, puppet version of Fabric properties are prefixed with cloudbiolinux_.

More information on Puppet can be found at:
https://puppetlabs.com/.
Bring in common puppetlabs Apache module as subrepo some dependent modules.
Add CloudBioLinux flavor for installing BioCloudCentral. This example is admittedly a little questionable as a first example of how to use the configuration management stuff since it is so far from CloudBioLinux's core competency (i.e. BioCloudCentral doesn't run bioinformatics software). It just happens that CloudBioLinux has become my hammer for deploying applications into the cloud, so BioCloudCentral looked like I nail. I promise I have some better examples lined up for the coming months that will mesh better with CloudBioLinux - globus integration, some proteomics web applications, and the LWR.

Right now there are is not a module for configuring postgres (though it would be nice to have it added) because I am using an external database. The database connection properties can be passed into puppet by defining the following fabric properties: puppet_biocloudcentral_db_host, puppet_biocloudcentral_db_port, puppet_biocloudcentral_db_password, puppet_biocloudcentral_db_user, puppet_biocloudcentral_db_name.
Update gitmodules that were pointing at @jmchilton repositories to point at @bioconfig repositories. If you want write access to @bioconfig repositories just send a message to @jmchilton.
Update bwa to the latest release
Update bwa to latest release