# this is the sample for the aa alphabet directory.
# when you copy to a new directory, change these values.
ALPHANAME ?= aa
ALPHADIR  ?= str2uc-near-backbone-11-20_rev
# watch out for this one. some files contain several alphabets.
# for example, str,str2,str3 are all defined in str.alphabet
# alphalibfile indicates the output alphabet ??
ALPHALIBFILE ?= combined-relabel.alphabet

# ARCHITECTURE ?= Gstr2uc_near_backbone_11_20-5-15-7-13-7-15-5
# ARCHITECTURE ?= Gstr2uc_near_backbone_11_20-7-30-3
# ARCHITECTURE ?= Gstr2uc_near_backbone_11_20-7-20-5-20-3
# ARCHITECTURE ?= Gstr2uc_near_backbone_11_20-3-20-5-20-7
# ARCHITECTURE ?= Gstr2uc_near_backbone_11_20-9-17-5-20-3
# ARCHITECTURE ?= Gstr2uc_near_backbone_11_20-5-30-3-20-3
# ARCHITECTURE ?= Gstr2uc_near_backbone_11_20-7-30-5-30-3
# ARCHITECTURE ?= Gstr2uc_near_backbone_11_20-9-20-5-20-3
 ARCHITECTURE ?= Gstr2uc_near_backbone_11_20-5-20-5-20-5
# ARCHITECTURE ?= Gstr2uc_near_backbone_11_20-3-29-3-29-3

TXXALIGN ?= str2uc-near-backbone-11-20

MAX_JOBS ?= 10

local-default: 
	echo run \"make trAB-mult50\" then wait for cluster to finish
	echo you can do \"make collect-mult50-data\" to see results of run
	echo run \"make trAB-mult150\" then wait for cluster to finish
	echo run \"make trAB-mult250\" then wait for cluster to finish
	echo run \"make trAB-test\" then wait for cluster to finish
	echo run \"make collect-test-data\"

nrm:
	rm -r net[0-9]* run-scripts/ logs/ quality-reports/

include ../Make.alphabet