Refactor wrapper functionality out of cgl-docker-lib

[nsjake]

The rna seq cgl wrapper.py file has two functions:

1. Docker specific functionality
2. Pipeline specific functionality
   Docker specific functionality is independent of any and all pipeline specific functionality. On the other hand pipeline specific functionality depends on this docker specific functionality. Since more pipeline specific functionality will be defined as other production workflows are dockerized, docker specific stuff needs to be moved to a shared location to prevent code duplication.

Second, the pipeline specific functionality corresponds closely with the definition of the particular pipeline in the toil-scripts repository. Often a change in toil-scripts/rnaseq-cgl requires changes in the corresponding wrapper script in cgl-docker-lib. This is an error prone approach.

The wrapper script should be removed from this repository and split into two places:

1. Docker specific functionality should refactored into its own repository.
2. Pipeline specific functionality should be refactored into a pipelines specific wrapper.py file and moved to some docker subdir of each pipeline repo. The Docker specific wrapper tool should be listed as a dependency of the pipeline repo and imported in the pipeline specific wrapper file.

This approach will have the added benefit of reducing the steps needed to set up the pipeline docker container as the wrapper will be installed with the pipeline itself.