clinseq - chmod on test file
Merge branch 'master' of ssh://git/srv/git/genome
Update submodule pointers for new tophat/bowtie.
handle has-many inputs gracefully on default software results
Merge branch 'master' of ssh://git/srv/git/genome
add paralleliz_by to Genome::Command::WithSavedResult
Switch htseq count to support many alignment results as input.  The parallelize_by flag is set on this, but it is still currently ignored.
Merge branch 'master' of ssh://git/srv/git/genome
Merge branch 'master' of ssh://git/srv/git/genome
fixed test after changing allowed tumor common names
Merge branch 'master' of ssh://git/srv/git/genome
added example_values to "gmt htseq count", and "where" filter, currently unused
ClinSeq - fix test plan for some converge tests
Merge branch 'master' of ssh://git/srv/git/genome
Updated Genome::Command::WithSavedResults to break inputs down and run N subordinate commands.  No mereg logic yet, and no workflow around the parts (not parallelized, just divided).
ClinSeq - Major update to convert scripts to command, wrap them in unit tests, and drop into the ClinSeq workflow
Cache substructures and fix some bugs
Initial attempt to generate an empty variants aspect for comparison.
Merge branch 'master' of ssh://git/srv/git/genome
refactor test and use compare_ok instead of diff