disable BQM
add Genome::Sys::Gateway and related command tree for working with other GMSs
Merge branch 'master' of ssh://git/srv/git/genome
Updated class browser cache.
Updated `genome` tab completion.
Updated class browser cache.
Updated `genome` tab completion.
blessed new clinseq build to match changes in LIMS
Merge branch 'master' of ssh://git/srv/git/genome
Add set_pipefail option to Genome::Sys->shellcmd

The default is to set_pipefail for compatibility but now
you can specify that you don't want pipefail set if you want to.
Stop using pipefail in PrepareInstrumentData

Having it set causes the Flow model tests to fail, even though (oddly
enough) it does not cause the Genome model tests to fail.  The Flow
model tests passes diff tests after running with this set, so we don't
think it is a mistake to turn off pipefail here.
updated metadata exporter to get feature lists, associated reference sequence builds, and adaptors between refseq builds
Changed the way in which temporary files are generated
simple integration test for the Mutect tool
remove an unnecessary test