GitLab

* version/1.9:
  made most of the tests in t/ runnable as standalone scripts

* version/1.9:
  Copied and adapted the test-suite from 2.3
  PostgreSQL doesn't know GROUP_CONCAT()

* version/1.9:
  bugfix [pgsql]: "argument of AND must be type boolean, not type integer"

bugfix: make sure the outer pair of quotes is removed as per bash rules (using a new function) -- thanks to Harpreet for reporting

bugfix: make sure the outer pair of quotes is removed as per bash rules (using a new function) -- thanks to Harpreet for reporting

compatibility fix: in LSF since version 9.1.2 job array index seems to be appended to the first column of bjobs output - thanks to Jan Vogel for reporting

compatibility fix: in LSF since version 9.1.2 job array index seems to be appended to the first column of bjobs output - thanks to Jan Vogel for reporting

* version/1.9:
  Capture errors from reading files / running commands in JobFactory

Check that the analysis is not BLOCKED before running a special-batch (i.e. runWorker with a job_id)

This is can be overriden with "-force 1"

* version/1.9:
  Better way of sharing the "take_time" parameter

* version/1.9:
  Made _add_together() a method so that we can die if input data are missing
  Renamed AnalysisStats::update() to update_stats_and_monitor() in order to restore the inherited update() method
  Added an option to accurately catch errors in pipes (needs bash to work)
  Use "bash -o pipefail" to make sure we catch errors on both sides of the pipe
  Explain that  is in minutes (but stored in secs)
  Set  (cause_of_death) to 'UNKNOWN' when not defined

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

* version/1.9:
  The batch-size is not set by the workers, so they shouldn't update it
  Only update hive_capacity in analysis_stats when in DYNAMIC mode

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

* version/1.9:
  bugfix: chunk_length and chunk_size must be updated at the same time the sequences are written (thank you @mn1 !)

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