clean up our temp space after we use it so we do not run out
move fastq files to temp_staging_directory to avoid filling up temp.  also, cleanup afterwards
rsids are optional and don't cause warnings if not there
Add error message for duplicate annotations
Merge branch 'updated' into gb_master
updated jenkins submodule to ad9380d
remove unused cruft
remove all the database stuff from these, since it no longer matters
clin-seq: further tweaks to snv-indel report graphics
don't check for child allocations during testing
Update blessed build for rnaseq test model

Jason Walker changed some metadata for its instrument data which lead to
different tophat args related to inner insert size
updated graphite submodule to 00ac7bb
Updated class browser cache.
Updated `genome` tab completion.
Still run the child query when testing allocations.
clin-seq - snv-indel-report - add gene labeling and variant tracking over time to plots
BWA AR: remove indexing ref in test
Revert "BWA AR: remove indexing ref in test"

This reverts commit 26f6cda8d7e07fea66423888fa6c08201484126c.
BWA AR: get or create aligner index
BWA AR: modernize and simplify test