RT673529 - Docker file locales fix

All locales are now installed into the docker image. A specific locale can be selected by passing, for example, --env LANG="en_GB.utf8" to the docker run command.

containerization bug fixes

Merge pull request #9 from trstickland/tweak_config_for_farm4

Tweak config for farm4

Sensible default and an ENV variable to set configuration file path

• Change default config path to /etc/gffmunger/gffmunger-config.yml
• Allow config file path to be set with environment variable GFFMUNGER_CONFIG
  Otherwise as before: looks in sys.prefix (i.e. where pip install would put it) or the GFFMunfer install directory (where git clone would put it).

Dockerfile and addition of optional commands

• Adds a Dockerfile
• Script now accepts a command, gffmunger [options] [command], that defines action to take; currently has only one function, to move annotations from polypeptide to mRNA (or other parent), and defaults to this if no command is specified. So ATM there's no extra functionality, but it provides a framework for adding new commands that invoke functions.

first sangerpathogens release

v0.0.1

fixed bug preventing proper logging ar levels lower than WARNING