relocate bam-errorrate and gtfToGenePhred to $GENOME_SW, and move hard-coded data paths to $GENOME_DB directories for CNV detection
make dbsnp file paths species-specific
Merge branch 'master' into pathfix
new tool to create clean assembly consensus file for allpaths assemblies
Merge branch 'master' of ssh://git/srv/git/genome
support new style BoolExpr which may not contain commas

Mirrors changed to Command::Dispatch::Shell in UR (65e8552, 9fa6cf1):

- Fixes bug that failed to parse "in clause" as a valid BoolExpr due to
  dependence on detecting BoolExpr by the presence '=', ':', or '~'.
- Remove broken feature, support for multiple data types.
- Removes support for list of BoolExpr statements, e.g.
  name=foo,name=bar.
- Moves exception throwing deeper since all practical exceptions would
  have been rethrown.
- Add some test coverage.
remove support for searching alternate classes when using boolexpr

Dot properties are a better solution that searching and we can't support
the "new" BoolExpr syntax while also supporting searching alternate
classes.
updated ur submodule to 65e8552
updated workflow submodule to a35c41e
fix tests that passed incorrect arguments to execution

A change to Command::V2 and Genome::Command::Base caused a bug to be
exposed in these tests.
ClinSeq - update all-events converge, minor bug fixes, add unit test for common lister commands
convert test to use Test::Builder::Tester
add run_ok
add capture_ok
avoid loading Genome::Model::Tools::Music::T when running `gmt music`

Since `gmt music` is a command it loads all modules underneath to
determine subcommand which trigger Genome::Model::Tools::Music::T to
load which a is a module used only for testing. That module was moved
into the `t` directory and renamed Test::Music to avoid this.
move Music/t to Music.t so contents won't be "monitored" by WebApp::Core
Merge branch 'master' into pathfix
fix to paths to executables merged
Merge branch 'pathfix' of ssh://git/srv/git/genome into pathfix
Merge branch 'pathfix' into gms-host

Conflicts:
	lib/perl-removed/Genome/Model/Tools/Music/T.pm
	lib/perl/Genome/Model/Tools/Music.t/Test/Music.pm
	lib/perl/Genome/Model/Tools/Music/T.pm