TODO: Allow annotations to be specified for all species in the file, not just the
'primary' organism (as specified by the dbkey). Metadata for sequences will need to be
fleshed out more first (i.e. store all species present in the file).
#) An "xy_plot" tool and a new "build_ucsc_custom_track" tool that
demonstrate the various features added here.
#) Grouping constructs for tool parameters:
- "repeat" element allows for a set of parameters to be repeated an
arbitrary number of times
- "conditional" element allows choosing a set of parameters to display
based on the value of another parameter
These constructs can be arbitrarily nested. Their values are structured
and can be used in hooks, validation, et cetera
#) Support for generating arbitrary config files to pass to a tool
#) Command lines are now full Cheetah templates
#) Better job error reporting, includes tracebacks for internal errors
preparing the job (database change required, see below!)
#) Preparation of command line, config files, exec_before_job hook moved
into job execution stage
#) Parameter values now jsonified before storing in database (this is much
more rigorous that before, and restoring from the database now works
properly)
DATABASE CHANGE:
alter table job add column traceback text;
Greg Von Kuster