FIX BUG: When requesting a specific job, the job was re-run until until the workers had run jobs for at least MIN_BATCH_TIME

as change it to use ensembl-analysis breaks other dependencies.

ensembl-pipeline as the later has been declared obsolete and modules have
been removed from the repository.

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