Changes to make QC work on farm3
Removed webapp_setup_shell from scrips as it is now in tope level.
Merge branch 'master' into dp10

Conflicts:
	lib/HTGT/QC/Util/KillQCFarmJobs.pm
	lib/HTGT/QC/Util/RunExonerate.pm
	lib/HTGT/QC/Util/SubmitQCFarmJob.pm