Change in the monitor table: analyses -> analysis to improve auto-completion in mysql client for all the analysis_* tables.

replaced the remove/delete analysis -- shouldnt be using that unless you know what you are doing -- not advertised in the help anymore -- Albert Vilella and Michael Schuster

the deletion of the method is done in the right place now - still, be careful about using this method - Albert Vilella and Michael Schuster

adding a remove_analysis_id method that will DELETE FROM analysis, analysis_stats, and analysis_job table WHERE analysis_id equals the number given

Change: performs global cleanup after a worker dies unless no global cleanup has been explicitly requested

Now takes into account lsf_pending jobs if any, before deciding to do a hard sync. Added specific exit message when beekeeper is running a specific analysis that is completed

very rare circumstances, caused error messages to be sent to space

size (flushes)

Committed Kathryn changes. Added runnable and output subroutine. These should make the coding of Bio::EnsEMBL::Analysis::RunnableDB and Bio::EnsEMBL::Hive::Process more alike.

When -logic_name is given, now only returns/creates the number of workers needed precisely for this analysis.

Added an optional Bio::EnsEMBL::Analysis argument to get_num_needed_workers subroutine, to only get the number of workers needed for this analysis

design element in Worker::batch_size
- old design: setting the batch_size for a worker changed the batch_size for
  all workers by updating the analysis_stats.batch_size of the corresponding
  analysis. Although this code was never triggered in the current system, it
  could have caused potential problems for future developers.
Now setting the batch_size explicitly for a worker only effects the
batch_size for that Worker instance. If it has not been set, the Worker pulls
the batch_size from the analysis_stats record and optionally autocalcs from
avg_msec_per_job if the batch_size<=0.

gets large

added a new debug printing of each job as such
  job_id=9050 blast_1_DEFAULT(17) retry=0 input_id='982'
if the worker has debug turned on

to use a logic_name rather than an analysis_id

  removed option -analysis_stats
  added option -no_analysis_stats

-regfile and -regname by default it looks for the alias 'hive' in the
registry if -regname is not specified

are neither done nor failed.  Changed print_stats to show remaining_job_count
instead of done.  Since this number now counts done to zero, it is much
easier to read how much work is left to do.

added check to test if system is DONE and stop the beekeeper if there is
nothing left to do.

jobs that were created outside the database.  Also added ability to not
write (doesn't execute write_output or dataflow jobs).  Improved logic so
that if a job is specified, but something is wrong that the worker fails
rather than reverting to autonomous behaviour mode.

runWorker.pl now provides much better debugging capability through the
use of the -logic_name, -input_id and -no_write combination.

Fully tested by running a complete homology production test.

jobs that were created outside the database.  Also added ability to not
write (doesn't execute write_output or dataflow jobs).  Improved logic so
that if a job is specified, but something is wrong that the worker fails
rather than reverting to autonomous behaviour mode.
Fully tested by running a complete homology production test.