Proteomics: Morpheus fixes for /usr installs (was working for Galaxy tool install).
Proteomics: Update to latest msconvert.
More debconf work toward fully automated install.
Proteomics: Add more required packages for RVM.
Proteomics: Specify absolute path for Galaxy-P tools file so it works with deployer. Also allow the path to be overridden with galaxyp_tool_conf.
PEP-8 fixes for cloudbio/custom/shared.py.
Allow cloudbiolinux work directory to be overridden with  in fabricrc.
Setup specified 'work_dir' using sudo - though only if needed, shouldn't cause any installs that were working without sudo to suddenly need it.

Amazon instances seem to have less root than my OpenStack instances so I ran out of space while installing Galaxy-P because of the large amount of space required by OpenMS. I can now just add 'work_dir = /mnt/cblwork' to fabricrc to get around this by using ephemeral disk. In theory, ephemeral disk should also be faster - though in practice but I haven't actually observed this.
More reorganization of Galaxy-P stuff, this time to allow a stand-alone install (without CloudMan) for desktop and traditional cluster environments.
Correctly install gemini when system install is a local directory
Deployer: Add --target_bucket to manually specify bucket for sync_cloudman_bucket action.
Deployer: Allow ${the_date} and ${the_date_with_time} to appear in cluster name for CloudMan.
Deployer: Expand cloudman_repository settings.yaml option to allow mercurial or git repository to be used as source. Additionally if git repositroy is used 'repository_branch' be also be supplied to clone down a specific branch for bundling.
Galaxy: Add 'provides' option to tool configuration to allow a package to be linked in as provide package dependencies for other packages. Use this to specify that the transproteomics pipeline install also install proteowizard and XTandem.
Deployer: Allow datetime substitution for snapshot descriptions.
Deployer: Add install_custom action and --package command-line argument (will also read from settings.yaml if command-line argument is unspecified).
Allow specification of image_user_data properties and CloudBioLinux deployer settings.yaml file. Add note about targetting AMI to a new bucket_default.
Remove some user_data defaults in example cloudman deployer settings file. Seemed to work without these when launching for BioCloudCentral for me so I guess they are not needed.
Deployer: Fixes for empty user_data in CloudMan section.
Deployer: Add --hostname argument.