updated jenkins submodule to f7bb6e7
updated jenkins submodule to 64f4416
rename to compare_ok but keep diff_ok as alias for now
refactor compare_ok's arg parsing

It might be overly complex but the goal was to work like Test::More
while also allowing additional options. Valid forms are:

- file_1, file_2
- file_1, file_2, test_name
- file_1, file_2, name => test_name, etc.
- file_1, file_2, filters => qr(//)
- file_1, file_2, filters => [qr(//), qr(//)]

filters was previously just filter.
add global option to line filter
remove unused use
switch a couple tests to use compare_ok
Added submodule cloneCaller
ClinSeq update to only warn about archived and set-do-not-archive status for last succeeded build
First commit of new SV annotator

This basically places the JWAnnot.pl script into a perl module,
preparing for future development.
Merge branch 'vep' into gb_master
Testing a theory about LSF state latency.
setup staging dir within the eval

Trying to close some gaps in allocation handling for RT #89047.
delete allocation if aborting

Trying to close some gaps in allocation handling for RT #89047.
delete allocation(s) if aborting

Trying to close some gaps in allocation handling for RT #89047.
check that directory paths are set

Since $self->output_dir is not populated until
$self->_prepare_output_directory is called someone could accidentally
call _promote_data before that.
Fixed the merged alignment result get so that multiple instrument data ids function.
Merge branch 'master' into gb_master
limit module_regex to .pm files
change status_message to debug_message