when first starting up farm mode we now delete dead runners; we also now have an alarm in the fork_call for starting up handlers, which will hopefully stop the server silently stalling out
Step post_process now throws on failure, which is cought by PipelineSetup trigger, which is now emailed out by the submission handler; we now emit behaviours for all states as they complete, even ones with same_submissions_as
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
increased memory requirement for gmap_build index building
handles fastq.gz file suffix correctly
automatic stepstate start_overs have been disabled to aid in debugging during production (!)
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
version bump
Merge branch 'release/0.120'
Merge branch 'release/0.120' into develop
mod to description
pass bam metadata to output
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
fix iget Tile dimensions
the handler fork call now kills itself after 15mins instead of 5, with a better error message; we now delete defunct runners from db and job scheduler
new only_not_started option to incomplete_element_states, to get only elementstates still at step 0
potential fix to the problem of datasource not updating with complex sources
pipelinesetup->trigger has new first_step_only option, used by setup handler; handler also now does the incomplete subs check regardless of there being fails, and also checks up on stuck same_submissions_as stepstates
automatic start_over for missing in/out files re-enabled
version bump