If passed as number mode gets converted to decimal, should be string
Ensure CloudMan and Galaxy packages are only added when building CloudBioLinux AMIs. Thanks to  Venkatesh Duvvuri
Merge pull request #157 from nuada/upstream

If passed as number mode gets converted to decimal, should be string
Move Homebrew installation after loading of brew packages. Enables skipping Homebrew install steps if no packages needed. Fixes #156
Handle finding flavor module if not suffixed with 'flavor'. Fixes #158
Don't reconfigure fabric env in fabfile.install_brew() if automated
install.

Without this fix, the env flavor is getting reset inside of
install_brew().
Merge pull request #159 from glebkuznetsov/master

Don't reconfigure fabric env in fabfile.install_brew() if automated install.
For remote env.safe_run_output disable shell by default
Not needed because of fixed env.safe_run_output
Merge pull request #160 from nuada/ls-color-fix

Fixed disabling of ls color output
Include Staden io_lib with support for CRAM indexing and retrieval by position
Attempt to work around hang when checking for leiningen during reprocessing
Add cramtools and rtg-tools support through brew installs. Remove old custom cramtools install