Fix for older fabric not having warn_only function in fabric.api module.
Deployer: Add more variants of deploy.sh. deploy_bourne attempts to set up dependencies using just sh compatible functionality (eliminate bash requirement). deploy_no_deps.sh expects to be called from deploy diretory and sets up no requirements. Galaxy team had problems with bash requirement - deploy_bourne.sh attempts to fix this. Had some complaints about virtualenv_burrito not working behind a proxy - the deploy_no_deps.sh should fix that (or at least allow a fix).
Merge @jmchilton's old vm-launcher into cloudbio.deploy. Eliminate need for git based dependency in requirements.txt for deployer. Centralize code making it easier to hack on.
Deployer: Bug fixes and clean up of deploy_bourne.sh.
Deployer: Bug fix, env.logger used before set.
I have a user (David Trudgian) who experienced some trouble using the local sudo installer behind a proxy.

He got it to work by adding the following lines to /etc/sudoers

    Defaults env_keep +="http_proxy"
    Defaults env_keep +="https_proxy"

I think this changeset may have the same effect (I'll see if he is willing to test it), but not require modifications to /etc/sudoers. If this is overly specific, feel free to pull this out and I will find a place to document modifing /etc/sudoers instead.
Provide local build and additional cleanup for rpy. #108
Avoid bcbio.variation jar downloads with AWS key information instead of jar name. Thanks to David McWillliams for report