GitLab

experimental: detect and bury the UNKWN workers -- the user takes responsibility by running -unkwn flag

bugfix: make sure dataflow rules are available to the beekeeper (which at the moment is collection-free)

bugfix: stop the Queen from finding buried-in-haste roles that are in fact linked to retried SEMAPHORED jobs

schema_change: a patch to include the live_roles view in the list of tables affected by drop_hive_tables

* ensembl-github/master:
  bugfix: round down the potentially non-integer hive_capacity-related limit
  bugfix: switching to using the newly created find_all_by_pattern() and collections in Worker to fix the -job_id bug
  find_all_by_pattern() is now supported on the collection level

bugfix: switching to using the newly created find_all_by_pattern() and collections in Worker to fix the -job_id bug

Merge remote-tracking branch 'ensembl-github/master' into python

* ensembl-github/master:
  moved mysql_use_result=>1 to the $sth_attribs hash
  allow capturing dataflow from a standaloneJob into a semaphored group
  Dataflow rules are stored in the Analysis, not the Job
  bugfix: make sure dataflown jobs are stored even in standalone mode
  generalized load_parameters() moved into AnalysisJob
  bugfix [to 97e17d94] : removed the leading zero from param_init call in gc_dataflow
  The $a syntax in #expr() has long gone, Should use #a# instead
  Deprecate --append in db_cmd.pl
  deprecated and removed support for strict_hash_format() method in Runnables
  We don't use $SKIP_TESTS in ensembl-hive

Conflicts:
	modules/Bio/EnsEMBL/Hive/Worker.pm
	t/10.pipeconfig/longmult.t