Conflicts:
	modules/Bio/EnsEMBL/Hive/Worker.pm

Conflicts:
	modules/Bio/EnsEMBL/Hive/Worker.pm

Conflicts:
	modules/Bio/EnsEMBL/Hive/Worker.pm

* version/2.1:
  cause_of_death can be undefined here (for local meadows, for instance)

* version/2.1:
  Backported the recent changes from Ensembl's DBConnection

* version/2.0:
  Backported the recent changes from Ensembl's DBConnection

- use placeholders in "do" commands

bugfix [to ee51e74e] : restore the password-hiding functionality between beekeeper.pl and runWorker.pl

* version/2.1:
  The main index is docs/index.html

Conflicts:
	docs/scripts/index.html

* version/2.0:
  The main index is docs/index.html

* version/1.9:
  The main index is docs/index.html

- always write the sequence to the current seqio - fix for creating lots of empty output files
- fix warning "Use of uninitialized value in subroutine entry"

- always write the sequence to the current seqio - fix for creating lots of empty output files
- fix warning "Use of uninitialized value in subroutine entry"

- always write the sequence to the current seqio - fix for creating lots of empty output files
- fix warning "Use of uninitialized value in subroutine entry"

PR #5

  bugfix: jobs could not trigger MEMLIMIT events
  bugfix: release the unfinished batch if the worker is contaminated

(and probably RUNLIMIT as well)
The problem was in Queen::register_worker_death(). The code fetches the
current role, finalizes it, and then updates the worker table. The role
that is fetched from the database with fetch_last_unfinished_by_worker_id()
is not connected to any workers and later, when
AnalysisJobAdaptor::release_undone_jobs_from_role() needs to know the cause
of death and the number of work done by the worker, the role would load
another instance of the worker using the information currently stored in
the database, that is: before it has been updated.
Hence, the code was complaining that cause_of_death was not populated.
By associating the role to the worker, we allow the method to read the
existing information

This is done by setting "self_burial" to 0

pulled in from version/2.1 : bugfix (long-standing) : make sure foreign jobs are created in the right database

bugfix: reload the list_of_analyses before each iteration of beekeeper, to be up to date with any changes