ClinSeq: Expand definition of tumor sample name
Merge branch 'master' of ssh://git/srv/git/genome
Replace shellcmd calls with direct calls to the lister.
Fix broken converge tool.  The test was turned off and marked as relying on data that does not exist.  This does not seem to be the case.  This test relies on a test model-group of only two models that was created specifically for this kind of test...  The test is passing.  Perhaps there was another problem with this test?
Merge branch 'master' of ssh://git/srv/git/genome
Replace shellcmd call with call to move_file
Replace shellcmd calls with copy_file calls.
Remove nonsensical shellcmd call with memory location.
Replace shellcmd calls with copy_file and perl's unlink.
Replace shellcmd calls with copy_file.
Replace shellcmd call with copy_file call.
Remove test code from production.
Replace shellcmd calls with direct calls to other commands.
Remove extraneous "use" statement--the autoloader will load this.
Remove unused Genome::Model::ClinSeq::Util import.
Remove duplicate 'use Genome;'
Remove duplicate 'use Genome;'
Remove extraneous "use Command;"
Remove extraneous "use Genome::Model::ClinSeq"
Remove unused Data::Dumper includes.