Merge pull request #56 from NationalGenomicsInfrastructure/master

Get Denis summer contributions.
Merge pull request #57 from NationalGenomicsInfrastructure/master

Get Denis clean-up changes
Merge pull request #58 from NationalGenomicsInfrastructure/master

get new stuff from Denis
Merge pull request #59 from NationalGenomicsInfrastructure/master

Further work by Denis
Changed name from application.py app_charon.py for easier maintanenance.
Merge pull request #48 from pekrau/master

Change name of application.py to app_charon.py