Bioboxes python interface library.

[michaelbarton]

I've extracted the biobox specific Python code the command line interface into a separate library library. This provides the option to create and run bioboxes from Python programs, this would sit between creating biobox containers directly using the docker client (more flexible, more effort) to using the command line interface (less flexible, less effort).

I added some additional functionality which I wanted in the nucleotid.es benchmarking client which may be of general use. This includes:

• a simplified way to create biobox containers. These containers can then be started using the container ID from any standard docker interface/library.
• ability to collect cgroup from a running container.
• automatic mapping of the biobox input file paths from the host file system to the container file system. This is something we have discussed previously. I.e. create a biobox input file where the paths are to the files on the host, these paths then get automatically remapped to directories in the container and the appropriate docker volume strings to do so are supplied.

I suggest the switch the command line interface be eventually switched over to use this library. All additional changes and updates would then ne implemented and tested in this library first, and then new versions can be rolled out using python's packaging system.