Remove unused somatic pipeline tools

Remove unused somatic pipeline stuff

Fix some tests that depended on somatic models
Merge branch 'updated2' into gb_master
Test should not overwrite files in test data directory
Merge branch 'updated2' into gb_master
Test shouldn't write into test data dir
Merge branch 'updated2' into gb_master
Removed obsolete model tests
Merge branch 'updated2' into gb_master
updated ur submodule to 6521360
updated jenkins submodule to 3319447
whitespace
limit test tracking
add test to replace `ur test use`
test_fail does not work when wrapped in a `do` (test-tracker)
shouldn't `do` a test
rename function to reflect fact that it does not perform a test
gmb view now shows calculated elapsed times in color
Add logic to show SoftwareResult Test Name in gmb view
Removed filesystem default
Removed default values for reference