GitLab

bugfix : update bjobs call in check_worker_is_alive_and_mine for compatibility with LSF 9.1.1.1, and eliminate call to system grep

bugfix: if the meadow is not reachable, there is no limiter for it (and the analysis cannot be scheduled)

bugfix: for the test-suite (and maybe some of our patched old pipelines) we should support pre-2016 dates

* Use File::Glob to get the list of filenames

Previously backtick ls command was used to fetch the list of sql patches filenames.
By using backtick it is required to fork a new process. This would potentially be
a problem for a running process that uses large amount of memory. If there is not
enough spare memory left in the system, the fork operation could be aborted because
of "cannot allocate memory" error.

Fixes ENSEMBL-4823.

bugfix: $? may be "contaminated" from another call. The best way is to check the trueness of the return value

Set the runnable's job earlier, so that error messages can be associated with the job in the log_message table

Turned the die statement into a warning (it is ok to do init_pipeline on a machine that doesn't see the farm)

bugfix: rounding the float before storing as an integer to avoid warnings; thanks to Michael Paulini for reporting