def main(): 
	parser = OptionParser(usage = "cn-avg_post_analysis_jobtree.py --cnavgout CN-AVG_outputdir --sampleid Sampleid --jobTree jobtreedir")
	
	add_analysis_options(parser)
	mcmcjobtree.add_mcmc_options(parser)
	Stack.addJobTreeOptions(parser)
	options, args = parser.parse_args()
	i = Stack(Setup(options)).startJobTree(options)
	if i: 
		raise RuntimeError("The jobtree contains %d failed jobs.\n" % i)
def main(): 
	parser = OptionParser(usage = "run_cn-avg_post_analysis_jobtree.py --samplelist samplelist.txt")
	parser.add_option("--samplelist", dest="samplelist", help="The list of CNAVG outputs and sample ids. Should have the form <directory><ID>")
	postjobtree.add_analysis_options(parser)
	mcmcjobtree.add_mcmc_options(parser)
	Stack.addJobTreeOptions(parser)
	options, args = parser.parse_args()
	i = Stack(Setup(options)).startJobTree(options)
	if i:
		raise RuntimeError("The jobtree contains %d failed jobs.\n" % i)