Merge branch 'release/0.165' into develop
check we still own the locks prior to running the job completion transaction, and warn and return on failure
no more database access during submission monitoring phase; exit when encountering an error in that phase after the submission is done; eval archive_output() which might be problematic - do not care about errors from it
json object now does convert_blessed, and Path::Class::* and Persistent objects now auto-convert, letting a number of tests that do not stringify their objects now pass
removed non-sensicle filetype error when the type was "any"; resolve_inputs also does a update_stats_from_disc() if necessary
adding test file needed by cufflinks.t
removed references to scratch102 in default settings
removing default script and data locations altogether
fixed StepRole _resolve_inputs() so that it no longer prevents mutli-filetype steps from working
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
fixed test to use verifyBamID in PATH
corrected number of tests to skip... this should probably be combined with gmap_build.t...
updated test expectations for bwa 0.6+
only cache _resolve_input_files results when more than 5 files
block_until_locked() now starts off checking every few 100th of a second before backing off to check_every value
in add_metadata() always reselect_values_from_db before transaction or we can lose metadata
protect against duplicate keyval/filelists by redis locking the lookup
version bump
Merge branch 'release/0.166'