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.