I needed to add in a check to prevent the worker from grabbing the same
job back and trying to run it again.  The retry works best when the job is
run on a different machine at a different moment in time (ie a different
hive_id).  This randomizes the run environment.

yet allow the worker to continue working.  Previous design killed the worker
when one of it's jobs fails.  This new design should be more efficient yet
still provide some level of inter-job-mangle-proof-ness.

but on a specific job.  For new system which catches job exceptions and
fails that job, but allows the worker to continue working.

to        eval "require Bio::EnsEMBL::Compara::DBSQL::DBAdaptor";

(taken from %self->input_job->dbID).

have not been run before (< retry_count)

don't have any ensembl-hive extensions.  To get access to extended hive functionality
one must inherit from Hive::Process.  A multiple inheritance is allowed like:
  our @ISA = qw( Bio::EnsEMBL::Hive::Process Bio::EnsEMBL::Pipeline::RunnableDB );

  into the Worker object (and out of the Process)
- added Process::worker method so that running processes can talk to the
  worker that is currently running itself.
- modified system so that if a process subclass uses Process::dataflow_output_id
  on branch_code 1, it will turn off the automatic of flowing of the input_job
  out on branch_code 1.  This will make coding much cleaner so that processes
  no longer need to modifiy the input_id of the input_job
- added method Process::autoflow_inputjob which toggles this autoflow behaviour
  if a subclass would like to modify this directly
- auto_dataflow now happens right after the Process::write_output stage

thus allowing one to do hybrid URL/Registry code like...
  if($url) {
    $dbc = Bio::EnsEMBL::Hive::URLFactory->fetch($url, 'compara')->dbc;
    $dbname = $dbc->dbname();
  }
  else { $dbc = Bio::EnsEMBL::Registry->get_DBAdaptor($dbname,'compara')->dbc; }
  $fa = Bio::EnsEMBL::Registry->get_adaptor($dbname,'compara','Family');

which is a simple paired file like.  If file is missing it does nothing
ia64e:3306      127.0.0.1:3371

-lsf_options <string>
which passes whatever is specified in the string to the bsub command
thus allowing the user complete flexibility

program has evolved into being the primary portal for user interaction
with the Hive, so 95% of functions are compute resource agnostic so it
makes more sense to have internal switches for which compute resource to
submit/check.  Expanded local logic to allow multiple local cpus, submit
into background(fork), check with 'ps', kill with 'kill -9'.

added columns hive_id and retry.  Allows user to join to failed workers
in the hive table, and to see which retry level the job was at when the
STDOUT/STDERR files were generated.  Sets at beginning of job run, and
deletes those for 'empty' files at job end.

in a more filesystem friendly manner (creates at 256 layer hash which distributes
the directories evenly and reduces concurrent directory modification.
Also reordered how the job output files are saved (done at the beginning right
after redirection starts, and at the end right before it's closed).

any problems related to setting undef or '0' values.

made the worse (Tim Cutts).  This will do until we figure this out....
I like the '>/dev/null + rerun failed jobs manually with debug' option personally :)

each digit becomes a directory with a final directory created with the full hive_id
hive_id=1234 => <base_dir>/1/2/3/4/hive_id_1234/
hive_id=12   => <base_dir>/1/2/hive_id_12/
this should distribute the output directories

is calculated.  If batch_size>0 use batch_size, else use avg_msec_per_job equation.

to RunnableDB to allow full benefit of dataflow graph capabilities.
- Removed from Extension.pm branch_code, analysis_job_id, reset_job extensions to
  RunnableDB (no longer trying to shoe-horn hive 'extra' functions into them)
- Bio::EnsEMBL::Hive::Process mirrors some of the RunnableDB interface
  (new, analysis, fetch_input, run, write_output)
  but uses a new job interface (input_job, dataflow_output_id) instead of
  input_id (but provides convenience method $self->input_id which redirects to
  $self->input_job->input_id to simplify porting)
- Changed Worker to only use hive 'extended' function if the processing module
  isa(Bio::EnsEMBL::Hive::Process).  Also allows all RunnableDB modules to
  still be used (or any object which implements a minimal 'RunnableDB interface')
  (new, input_id, db, fetch_input, run, write_output)

reordered where the blocking checks are done (added, deleted, moved).

needed workers after this worker is done.  Useful in debugging one's dataflow
and blocking_ctrl graphs by running one worker at a time (like stepping in a debugger)

a job that has been flowed into an analysis/process

added option -no_pend which ignores the pending_count when figuring out how many workers to submit
removed some superfluous calls to Queen::get_num_running_workers