GitLab

Renamed AnalysisStats::update() to update_stats_and_monitor() in order to restore the inherited update() method

This way, we avoid overriding values set by an external source (a human,
for instance)

bugfix: chunk_length and chunk_size must be updated at the same time the sequences are written (thank you @mn1 !)

(cherry-picked from version/2.1 branch)

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

Doxygen doesn't like when a =head2 section is not linked to a method.
We had to move the comments to #-prefixed lines.

bugfix: make sure that when multiple users are running the same pipeline on LSF, the numbers of their pending jobs are computed independently -- thanks, Mateus!

The worker_temp_directory for standalone workers was set to
/tmp/worker_${USER}.standalone. If two standalone workers were running
on the machine, they could overwrite each other’s files.
The fix include the process ID ($$ in Perl) in the directory name.

cosmetic: added deprecated message to CreateNewJob() and some documentation to store_jobs_and_adjust_counters()

store_jobs_and_adjust_counters() now also deals with semaphore_count corrections. It is now the preferred job-creation interface.

bugfix: no hope for other DBD drivers to support detection of auto-incrementing fields => use our inernal fixed rule

bugfix: stop printing overflow-related debug output to STDOUT; interface with overflow adaptor simplified