Add tree handler class for use in analysis project config
Merge branch 'master' of ssh://git/srv/git/genome
Updated `genome` tab completion.
Updated `genome` tab completion.
Updated `gmt` tab completion.
add YAML parser to use in analysis project config
1.add condition of empty contig.fasta for som-val pipeline; 2. bug fix for samtools mpileup snv vcf converter
Slightly clearer error when versions are a problem
Merge branch 'master' into gb_master
made --referene option required now
Merge branch 'master' of ssh://git/srv/git/genome
get logs from workflow instead of parsing bjobs
allow commands to specify the max_elapsed_log_time
set "RnaSeq Alignment" to allow 7 days for max_elapsed_log_time
Merge branch 'heartbeat'
add TreeCopy strategy for use in analysis configuration
remove breakpoint, whoops
remove _lock_model_for_start

It doesn't do anything to prevent duplicate builds but does cause
intermittent failures when trying to start test models under different
configurations.
add MaskedConfigurationReader to use in Analysis configuration
move _sync_database shortcut closer to source of problem

This @changed_objects "shortcut" is to avoid an issue with autocommit on the Pg
driver where it would cause an unwanted lock.  This was previously in
Command::Dispatch::Shell from UR commit 7fd973b.