Move string args tweaking into subroutine
Make accessor functions rather than local variables
Extract custom_args method
Extract methods for plugin_args and cache_args
Extract method for db_connect params
Extract methods to construct and run the command
Extract method to get or create the temp dir
Create one plugin arg string at a time
Separate staging plugin config from querying for plugin args
Add vep plugin object
Make transient properties Text instead of String

This way they don't get slurped in as string properties
Use plugin object
whitespace
Move stage method to cache object
Put most functionality into a base class
Add a new interface to vep command

Gets the api and cache through the ensembl version
instead of the annotation build
Merge branch 'updated' into gb_master