# These macros must be set by caller. these are examples
#
# ALPHANAME = bys
# ALPHADIR  = bys
# ALPHALIBFILE = bystroff.alphabet

MAX_JOBS ?= 5

TESTING = /projects/compbio/experiments/protein-predict/predict-2nd/testing
MAKE_PARA = ${TESTING}/Make.para


CHAIN = $(notdir $(shell pwd))

ifndef ALPHANAME
  $(error Error: ALPHANAME must be set. Usually this is done in the alphabet directory Makefile.)
endif
ifndef ALPHADIR
  $(error Error: ALPHADIR must be set. Usually this is done in the alphabet directory Makefile.)
endif
ifndef ALPHALIBFILE
  $(error Error: ALPHALIBFILE must be set. Usually this is done in the alphabet directory Makefile.)
endif

# These macros have defaults but can be overridden by caller
ifndef ARCHITECTURE
# current default architecture:       
       ARCHITECTURE=IDGaaH13-3-13-7-13-9-13-11
# older architecture used before guide sequences available
#      ARCHITECTURE=IDaaHr-5-15-7-15-9-15-13
# newer, experimental architectures with entropy and prob_of_guide
#      ARCHITECTURE=IDGEPaaH13-3-13-7-13-9-13-11
#      ARCHITECTURE=IDGEPaaH13-3-20-7-20-9-20-11
endif

ifndef DATASET
#      DATASET      = dunbrack-in-scop
       DATASET      = dunbrack-30pc-1763
endif

ifndef NET-NUM
       NET-NUM      = 100
endif

ifndef NET-START
       NET-START = 1
endif

ifndef PARAMFILE
#       PARAMFILE    = 16-dec-01-anneal
       PARAMFILE    = 7-jul-05.params
endif

ifndef TXXALIGN
       TXXALIGN     = t06-thin90
#      TXXALIGN     = t04-thin90
#      TXXALIGN     = t2k-thin90
endif

ifndef PREDICT-2ND
	PREDICT-2ND	= /projects/compbio/bin/i686/predict-2nd
endif

ifndef CLUSTER
	CLUSTER      = bmecluster
endif

ifndef NETS
	NETS = fullset.nets
endif

default:
	@echo There is no default behavior for this makefile

PCEM := /projects/compbio/experiments/models.97
PCEM_SCRIPTS := ${PCEM}/scripts
PARA_TRICKLE = ${PCEM_SCRIPTS}/para-trickle-make
SERIAL_MAKE = ${PCEM_SCRIPTS}/serial-make

DO_SERIAL ?=	${SERIAL_MAKE}  -makefile ${MAKE_PARA} -nouse_subdir -modelsdir ${TESTING}/${ALPHADIR}
DO_PARALLEL ?=  ${PARA_TRICKLE} -se2log -cluster ${CLUSTER} -manyids -rmvdir -makefile ${MAKE_PARA} -nouse_subdir -modelsdir ${TESTING}/${ALPHADIR}

SUBST :=  sed -e "s/ALPHANAME/${ALPHANAME}/"  | \
          sed -e "s/ALPHALIBFILE/${ALPHALIBFILE}/"  | \
          sed -e "s/PARAMFILE/${PARAMFILE}/"  | \
          sed -e "s/DATASET/${DATASET}/"  | \
          sed -e "s/TXXALIGN/${TXXALIGN}/"  | \
          sed -e "s/ARCHITECTURE/${ARCHITECTURE}/"  

PASS_DOWN := TXXALIGN=${TXXALIGN} ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET}

T1C2-SCRIPT = run-scripts/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-t1c2-${ALPHANAME}-from-empty.script
T2C3-SCRIPT = run-scripts/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-t2c3-${ALPHANAME}-from-empty.script
T3C1-SCRIPT = run-scripts/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-t3c1-${ALPHANAME}-from-empty.script

TR12-SCRIPT = run-scripts/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-${ALPHANAME}-from-empty.script
TR23-SCRIPT = run-scripts/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-${ALPHANAME}-from-empty.script
TR31-SCRIPT = run-scripts/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-${ALPHANAME}-from-empty.script


# this target makes 3 scripts that use one-third each for train, cross-train, test
# first set of commands makes most of the variable substitutions
# then 3 sets of commands make the substitutions for the combinations of thirds
tAcB.scripts:
	cat ../run-scripts/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.template.script | \
	  ${SUBST} | \
          sed -e "s/TRAINORCROSS/cross-train/"  | \
          cat > run-scripts/tmp.THIRDStAcB.script
	cat run-scripts/tmp.THIRDStAcB.script | \
          sed -e "s/THIRDSNAME/t1c2/"  | \
          sed -e "s/THIRDSA/1/"  | \
          sed -e "s/THIRDSB/2/"  | \
          sed -e "s/THIRDSC/3/"  | \
          cat > ${T1C2-SCRIPT}
	cat run-scripts/tmp.THIRDStAcB.script | \
          sed -e "s/THIRDSNAME/t2c3/"  | \
          sed -e "s/THIRDSA/2/"  | \
          sed -e "s/THIRDSB/3/"  | \
          sed -e "s/THIRDSC/1/"  | \
          cat > ${T2C3-SCRIPT}
	cat run-scripts/tmp.THIRDStAcB.script | \
          sed -e "s/THIRDSNAME/t3c1/"  | \
          sed -e "s/THIRDSA/3/"  | \
          sed -e "s/THIRDSB/1/"  | \
          sed -e "s/THIRDSC/2/"  | \
          cat > ${T3C1-SCRIPT}
	rm -f run-scripts/tmp.THIRDStAcB.script

# this target makes 3 scripts that use two-thirds for train, one-third for test
# first set of commands makes most of the variable substitutions
# then 3 sets of commands make the substitutions for the combinations of thirds
trAB.scripts:
	cat ../run-scripts/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-from-empty.template.script | \
          ${SUBST}  | \
          sed -e "s/TRAINORCROSS/train/"  | \
          cat > run-scripts/tmp.THIRDStrAB.script
	cat run-scripts/tmp.THIRDStrAB.script | \
          sed -e "s/THIRDSNAME/tr12/"  | \
          sed -e "s/THIRDSA/1/"  | \
          sed -e "s/THIRDSB/2/"  | \
          sed -e "s/THIRDSC/3/"  | \
          cat > run-scripts/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-${ALPHANAME}-from-empty.script
	cat run-scripts/tmp.THIRDStrAB.script | \
          sed -e "s/THIRDSNAME/tr23/"  | \
          sed -e "s/THIRDSA/2/"  | \
          sed -e "s/THIRDSB/3/"  | \
          sed -e "s/THIRDSC/1/"  | \
          cat > run-scripts/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-${ALPHANAME}-from-empty.script
	cat run-scripts/tmp.THIRDStrAB.script | \
          sed -e "s/THIRDSNAME/tr31/"  | \
          sed -e "s/THIRDSA/3/"  | \
          sed -e "s/THIRDSB/1/"  | \
          sed -e "s/THIRDSC/2/"  | \
          cat > run-scripts/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-${ALPHANAME}-from-empty.script
	rm -f run-scripts/tmp.THIRDStrAB.script


run-tAcB:
	${PARA_TRICKLE} -cluster ${CLUSTER} -rmvdir -quick '${PREDICT-2ND} < ${T1C2-SCRIPT} >& logs/${TXXALIGN}-${ARCHITECTURE}-T1C2.log'
	${PARA_TRICKLE} -cluster ${CLUSTER} -rmvdir -quick '${PREDICT-2ND} < ${T2C3-SCRIPT} >& logs/${TXXALIGN}-${ARCHITECTURE}-T2C3.log'
	${PARA_TRICKLE} -cluster ${CLUSTER} -rmvdir -quick '${PREDICT-2ND} < ${T3C1-SCRIPT} >& logs/${TXXALIGN}-${ARCHITECTURE}-T3C1.log'

run-trAB:
	${PARA_TRICKLE} -cluster ${CLUSTER} -rmvdir -quick '${PREDICT-2ND} < ${TR12-SCRIPT} >& logs/${TXXALIGN}-${ARCHITECTURE}-TR12.log'
	${PARA_TRICKLE} -cluster ${CLUSTER} -rmvdir -quick '${PREDICT-2ND} < ${TR23-SCRIPT} >& logs/${TXXALIGN}-${ARCHITECTURE}-TR23.log'
	${PARA_TRICKLE} -cluster ${CLUSTER} -rmvdir -quick '${PREDICT-2ND} < ${TR31-SCRIPT} >& logs/${TXXALIGN}-${ARCHITECTURE}-TR31.log'

## 
## This starts the section for creating many random starts for creating
## neural networks,
## 

DIRS = ${addprefix net, $(shell seq ${NET-START} ${NET-NUM})}

tAcB-mult.scripts:
	$(foreach dir, ${DIRS}, \
		-mkdir networks/$(dir); \
		-mkdir run-scripts/$(dir); \
		-mkdir logs/$(dir); \
		-mkdir quality-reports/$(dir); \
	cat ../run-scripts/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-MULT-from-empty.template.script | \
          ${SUBST}  | \
          sed -e "s/TRAINORCROSS/cross-train/"  | \
          sed -e "s/NETNUM/$(dir)/" | \
          cat > run-scripts/tmp.THIRDStAcB.script ; \
	cat run-scripts/tmp.THIRDStAcB.script | \
          sed -e "s/THIRDSNAME/t1c2/"  | \
          sed -e "s/THIRDSA/1/"  | \
          sed -e "s/THIRDSB/2/"  | \
          sed -e "s/THIRDSC/3/"  | \
          cat > ${T1C2-MULT-SCRIPT} ; \
	cat run-scripts/tmp.THIRDStAcB.script | \
          sed -e "s/THIRDSNAME/t2c3/"  | \
          sed -e "s/THIRDSA/2/"  | \
          sed -e "s/THIRDSB/3/"  | \
          sed -e "s/THIRDSC/1/"  | \
          cat > ${T2C3-MULT-SCRIPT} ; \
	cat run-scripts/tmp.THIRDStAcB.script | \
          sed -e "s/THIRDSNAME/t3c1/"  | \
          sed -e "s/THIRDSA/3/"  | \
          sed -e "s/THIRDSB/1/"  | \
          sed -e "s/THIRDSC/2/"  | \
          cat > ${T3C1-MULT-SCRIPT} ; \
	rm -f run-scripts/tmp.THIRDStAcB.script;)
		
run-mult-tAcB:
	$(foreach dir, ${DIRS}, \
	${PARA_TRICKLE}  -rmvdir -quick '${PREDICT-2ND} < ${T1C2-MULT-SCRIPT} >& logs/$(dir)/${TXXALIGN}-${ARCHITECTURE}-T1C2.log'; \
	${PARA_TRICKLE}  -rmvdir -quick '${PREDICT-2ND} < ${T2C3-MULT-SCRIPT} >& logs/$(dir)/${TXXALIGN}-${ARCHITECTURE}-T2C3.log'; \
	${PARA_TRICKLE}  -rmvdir -quick '${PREDICT-2ND} < ${T3C1-MULT-SCRIPT} >& logs/$(dir)/${TXXALIGN}-${ARCHITECTURE}-T3C1.log';)
	
tAcB-mult-train.scripts:
	$(foreach dir, ${DIRS}, \
	cat ../run-scripts/DATASET-TXXALIGN-ARCHITECTURE-THIRDSNAME-ALPHANAME-MULT-for-testing.template.script | \
          ${SUBST}  | \
          sed -e "s/NETNUM/$(dir)/" | \
          cat > run-scripts/tmp.THIRDStAcB.script ; \
	cat run-scripts/tmp.THIRDStAcB.script | \
          sed -e "s/THIRDSNAME/t1c2/"  | \
          sed -e "s/THIRDSA/1/"  | \
          sed -e "s/THIRDSB/2/"  | \
          sed -e "s/THIRDSC/3/"  | \
          cat > ${T1C2-MULT-TRAIN-SCRIPT} ; \
	cat run-scripts/tmp.THIRDStAcB.script | \
          sed -e "s/THIRDSNAME/t2c3/"  | \
          sed -e "s/THIRDSA/2/"  | \
          sed -e "s/THIRDSB/3/"  | \
          sed -e "s/THIRDSC/1/"  | \
          cat > ${T2C3-MULT-TRAIN-SCRIPT} ; \
	cat run-scripts/tmp.THIRDStAcB.script | \
          sed -e "s/THIRDSNAME/t3c1/"  | \
          sed -e "s/THIRDSA/3/"  | \
          sed -e "s/THIRDSB/1/"  | \
          sed -e "s/THIRDSC/2/"  | \
          cat > ${T3C1-MULT-TRAIN-SCRIPT} ; \
	rm -f run-scripts/tmp.THIRDStAcB.script;)

run-mult-train-tAcB:
	$(foreach dir, ${DIRS}, \
	${PREDICT-2ND} < ${T1C2-MULT-TRAIN-SCRIPT} >& logs/$(dir)/${TXXALIGN}-${ARCHITECTURE}-train-T1C2.log; \
	${PREDICT-2ND} < ${T2C3-MULT-TRAIN-SCRIPT} >& logs/$(dir)/${TXXALIGN}-${ARCHITECTURE}-train-T2C3.log; \
	${PREDICT-2ND} < ${T3C1-MULT-TRAIN-SCRIPT} >& logs/$(dir)/${TXXALIGN}-${ARCHITECTURE}-train-T3C1.log;)

T1C2-MULT-SCRIPT = run-scripts/$(dir)/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-t1c2-${ALPHANAME}-from-empty.script
T2C3-MULT-SCRIPT = run-scripts/$(dir)/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-t2c3-${ALPHANAME}-from-empty.script
T3C1-MULT-SCRIPT = run-scripts/$(dir)/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-t3c1-${ALPHANAME}-from-empty.script

T1C2-MULT-TRAIN-SCRIPT = run-scripts/$(dir)/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-t1c2-${ALPHANAME}-for-training.script
T2C3-MULT-TRAIN-SCRIPT = run-scripts/$(dir)/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-t2c3-${ALPHANAME}-for-training.script
T3C1-MULT-TRAIN-SCRIPT = run-scripts/$(dir)/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-t3c1-${ALPHANAME}-for-training.script

collect-cross-train-data:
	../run-scripts/collect-data -number ${NET-NUM} -txxalign ${TXXALIGN} -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -ctrain 1 -data t1c2 > quality-reports/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-t1c2-mult-${ALPHANAME}.rdb
	../run-scripts/collect-data -number ${NET-NUM} -txxalign ${TXXALIGN} -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -ctrain 1 -data t2c3 > quality-reports/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-t2c3-mult-${ALPHANAME}.rdb
	../run-scripts/collect-data -number ${NET-NUM} -txxalign ${TXXALIGN} -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -ctrain 1 -data t3c1 > quality-reports/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-t3c1-mult-${ALPHANAME}.rdb


trAB-mult50: 
	${MAKE} ${PASS_DOWN} dirs
	${MAKE} ${PASS_DOWN} trAB-mult50.scripts 
	${MAKE} ${PASS_DOWN} trAB-mult50.run
trAB-mult150:
	${MAKE} ${PASS_DOWN} collect-mult50-data
	${MAKE} ${PASS_DOWN} trAB-mult150.scripts
	${MAKE} ${PASS_DOWN} trAB-mult150.run
trAB-mult250:
	${MAKE} ${PASS_DOWN} collect-mult150-data
	${MAKE} ${PASS_DOWN} trAB-mult250.scripts
	${MAKE} ${PASS_DOWN} trAB-mult250.run
trAB-test:	
	${MAKE} ${PASS_DOWN} collect-mult250-data
	${MAKE} ${PASS_DOWN} trAB-test.scripts
	${MAKE} ${PASS_DOWN} trAB-test.run

dirs:
	-mkdir logs
	-mkdir quality-reports
	-mkdir run-scripts
	-mkdir networks
	${DO_SERIAL} -targets '${PASS_DOWN} mult50.dirs' < ../training-data/${NETS} 

# Mon Nov 15 22:48:49 PST 2010 Kevin Karplus
# Replaced following parallel call with serial make
#	${DO_PARALLEL} -targets '${PASS_DOWN} mult50.dirs' < ../training-data/${NETS} &

trAB-mult50.scripts:
	${DO_SERIAL} -targets '${PASS_DOWN} mult50.scripts' < ../training-data/${NETS}

# Mon Nov 15 22:48:49 PST 2010 Kevin Karplus
# Replaced following parallel call with a serial make
#	${DO_PARALLEL} -targets '${PASS_DOWN} mult50.scripts' < ../training-data/${NETS}



trAB-mult50.run:
	${PARA_TRICKLE} -se2log -cluster ${CLUSTER} -manyids -max_jobs ${MAX_JOBS} -rmvdir -makefile ${MAKE_PARA} -nouse_subdir -modelsdir ${TESTING}/${ALPHADIR} -targets '${PASS_DOWN} mult50-tr12.run' < ../training-data/${NETS}
	${PARA_TRICKLE} -se2log -cluster ${CLUSTER} -manyids -max_jobs ${MAX_JOBS} -rmvdir -makefile ${MAKE_PARA} -nouse_subdir -modelsdir ${TESTING}/${ALPHADIR} -targets '${PASS_DOWN} mult50-tr23.run' < ../training-data/${NETS}
	${PARA_TRICKLE} -se2log -cluster ${CLUSTER} -manyids -max_jobs ${MAX_JOBS} -rmvdir -makefile ${MAKE_PARA} -nouse_subdir -modelsdir ${TESTING}/${ALPHADIR} -targets '${PASS_DOWN} mult50-tr31.run' < ../training-data/${NETS}
	
collect-mult50-data:
	../run-scripts/collect-data50 -number ${NET-NUM} -txxalign ${TXXALIGN} -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -ctrain 1 -data tr12 > quality-reports/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-mult50-${ALPHANAME}.rdb
	../run-scripts/collect-data50 -number ${NET-NUM} -txxalign ${TXXALIGN} -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -ctrain 1 -data tr23 > quality-reports/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-mult50-${ALPHANAME}.rdb
	../run-scripts/collect-data50 -number ${NET-NUM} -txxalign ${TXXALIGN} -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -ctrain 1 -data tr31 > quality-reports/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-mult50-${ALPHANAME}.rdb

trAB-mult150.scripts:
	${DO_SERIAL} -targets '${PASS_DOWN} mult150-tr12.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-${ALPHANAME}-mult50.nets
	${DO_SERIAL} -targets '${PASS_DOWN} mult150-tr23.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-${ALPHANAME}-mult50.nets
	${DO_SERIAL} -targets '${PASS_DOWN} mult150-tr31.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-${ALPHANAME}-mult50.nets

trAB-mult150.run:
	${PARA_TRICKLE} -se2log -cluster ${CLUSTER} -manyids -max_jobs ${MAX_JOBS} -rmvdir -makefile ${MAKE_PARA} -nouse_subdir -modelsdir ${TESTING}/${ALPHADIR} -targets '${PASS_DOWN} mult150-tr12.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-${ALPHANAME}-mult50.nets
	${PARA_TRICKLE} -se2log -cluster ${CLUSTER} -manyids -max_jobs ${MAX_JOBS} -rmvdir -makefile ${MAKE_PARA} -nouse_subdir -modelsdir ${TESTING}/${ALPHADIR} -targets '${PASS_DOWN} mult150-tr23.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-${ALPHANAME}-mult50.nets
	${PARA_TRICKLE} -se2log -cluster ${CLUSTER} -manyids -max_jobs ${MAX_JOBS} -rmvdir -makefile ${MAKE_PARA} -nouse_subdir -modelsdir ${TESTING}/${ALPHADIR} -targets '${PASS_DOWN} mult150-tr31.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-${ALPHANAME}-mult50.nets

collect-mult150-data:
	../run-scripts/collect-data150 -txxalign ${TXXALIGN} -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -data tr12 < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-${ALPHANAME}-mult50.nets > quality-reports/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-mult150-${ALPHANAME}.rdb
	../run-scripts/collect-data150 -txxalign ${TXXALIGN} -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -data tr23 < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-${ALPHANAME}-mult50.nets > quality-reports/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-mult150-${ALPHANAME}.rdb
	../run-scripts/collect-data150 -txxalign ${TXXALIGN} -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -data tr31 < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-${ALPHANAME}-mult50.nets > quality-reports/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-mult150-${ALPHANAME}.rdb

trAB-mult250.scripts:
	${DO_SERIAL} -targets '${PASS_DOWN} mult250-tr12.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-${ALPHANAME}-mult150.nets
	${DO_SERIAL} -targets '${PASS_DOWN} mult250-tr23.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-${ALPHANAME}-mult150.nets
	${DO_SERIAL} -targets '${PASS_DOWN} mult250-tr31.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-${ALPHANAME}-mult150.nets

trAB-mult250.run:
	${DO_PARALLEL} -targets '${PASS_DOWN} mult250-tr12.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-${ALPHANAME}-mult150.nets
	${DO_PARALLEL} -targets '${PASS_DOWN} mult250-tr23.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-${ALPHANAME}-mult150.nets
	${DO_PARALLEL} -targets '${PASS_DOWN} mult250-tr31.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-${ALPHANAME}-mult150.nets

collect-mult250-data:
	../run-scripts/collect-data250 -txxalign ${TXXALIGN} -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -data tr12 < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-${ALPHANAME}-mult150.nets > quality-reports/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-mult250-${ALPHANAME}.rdb
	../run-scripts/collect-data250 -txxalign ${TXXALIGN} -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -data tr23 < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-${ALPHANAME}-mult150.nets > quality-reports/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-mult250-${ALPHANAME}.rdb
	../run-scripts/collect-data250 -txxalign ${TXXALIGN} -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -data tr31 < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-${ALPHANAME}-mult150.nets > quality-reports/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-mult250-${ALPHANAME}.rdb

trAB-test.scripts:
	${DO_SERIAL} -targets '${PASS_DOWN} test-tr12.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-${ALPHANAME}-mult250.nets
	${DO_SERIAL} -targets '${PASS_DOWN} test-tr23.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-${ALPHANAME}-mult250.nets
	${DO_SERIAL} -targets '${PASS_DOWN} test-tr31.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-${ALPHANAME}-mult250.nets

trAB-test.run:
	${DO_PARALLEL} -targets '${PASS_DOWN} test-tr12.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-${ALPHANAME}-mult250.nets
	${DO_PARALLEL} -targets '${PASS_DOWN} test-tr23.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-${ALPHANAME}-mult250.nets
	${DO_PARALLEL} -targets '${PASS_DOWN} test-tr31.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-${ALPHANAME}-mult250.nets

collect-test-data:
	../run-scripts/collect-data-test -txxalign ${TXXALIGN} -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} > quality-reports/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-${ALPHANAME}-test.results

trAB-train-rdb.scripts:
	${DO_SERIAL} -targets '${PASS_DOWN} train-rdb-tr12.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-${ALPHANAME}-mult250.nets
	${DO_SERIAL} -targets '${PASS_DOWN} train-rdb-tr23.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-${ALPHANAME}-mult250.nets
	${DO_SERIAL} -targets '${PASS_DOWN} train-rdb-tr31.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-${ALPHANAME}-mult250.nets

trAB-train-rdb.run:
	${DO_SERIAL} -targets '${PASS_DOWN} train-rdb-tr12.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-${ALPHANAME}-mult250.nets
	${DO_SERIAL} -targets '${PASS_DOWN} train-rdb-tr23.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-${ALPHANAME}-mult250.nets
	${DO_SERIAL} -targets '${PASS_DOWN} train-rdb-tr31.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-${ALPHANAME}-mult250.nets


trAB-test-rdb.scripts:
	${DO_SERIAL} -targets '${PASS_DOWN} test-rdb-tr12.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-${ALPHANAME}-mult250.nets
	${DO_SERIAL} -targets '${PASS_DOWN} test-rdb-tr23.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-${ALPHANAME}-mult250.nets
	${DO_SERIAL} -targets '${PASS_DOWN} test-rdb-tr31.scripts' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-${ALPHANAME}-mult250.nets

trAB-test-rdb.run:
	${DO_SERIAL} -targets '${PASS_DOWN} test-rdb-tr12.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr12-${ALPHANAME}-mult250.nets
	${DO_SERIAL} -targets '${PASS_DOWN} test-rdb-tr23.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr23-${ALPHANAME}-mult250.nets
	${DO_SERIAL} -targets '${PASS_DOWN} test-rdb-tr31.run' < networks/${DATASET}-${TXXALIGN}-${ARCHITECTURE}-tr31-${ALPHANAME}-mult250.nets


#start of single sequence information

trAB-single-mult50.scripts:
	${DO_PARALLEL} -targets '${PASS_DOWN} mult50-single.scripts' < ../training-data/${NETS}


trAB-single-mult50.run:
	${PARA_TRICKLE} -se2log -cluster ${CLUSTER} -manyids -rmvdir -max_jobs ${MAX_JOBS} -makefile ${MAKE_PARA} -nouse_subdir -modelsdir ${TESTING}/${ALPHADIR} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult50-single-tr12.run' < ../training-data/${NETS}
	${PARA_TRICKLE} -se2log -cluster ${CLUSTER} -manyids -rmvdir -max_jobs ${MAX_JOBS} -makefile ${MAKE_PARA} -nouse_subdir -modelsdir ${TESTING}/${ALPHADIR} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult50-single-tr23.run' < ../training-data/${NETS}
	${PARA_TRICKLE} -se2log -cluster ${CLUSTER} -manyids -rmvdir -max_jobs ${MAX_JOBS} -makefile ${MAKE_PARA} -nouse_subdir -modelsdir ${TESTING}/${ALPHADIR} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult50-single-tr31.run' < ../training-data/${NETS}
	
collect-single-mult50-data:
	../run-scripts/collect-data50 -number ${NET-NUM} -txxalign single -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -ctrain 1 -data tr12 > quality-reports/${DATASET}-single-${ARCHITECTURE}-tr12-mult50-${ALPHANAME}.rdb
	../run-scripts/collect-data50 -number ${NET-NUM} -txxalign single -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -ctrain 1 -data tr23 > quality-reports/${DATASET}-single-${ARCHITECTURE}-tr23-mult50-${ALPHANAME}.rdb
	../run-scripts/collect-data50 -number ${NET-NUM} -txxalign single -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -ctrain 1 -data tr31 > quality-reports/${DATASET}-single-${ARCHITECTURE}-tr31-mult50-${ALPHANAME}.rdb

trAB-single-mult150.scripts:
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult150-single-tr12.scripts' < networks/${DATASET}-single-${ARCHITECTURE}-tr12-${ALPHANAME}-mult50.nets
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult150-single-tr23.scripts' < networks/${DATASET}-single-${ARCHITECTURE}-tr23-${ALPHANAME}-mult50.nets
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult150-single-tr31.scripts' < networks/${DATASET}-single-${ARCHITECTURE}-tr31-${ALPHANAME}-mult50.nets

trAB-single-mult150.run:
	${PARA_TRICKLE} -se2log -cluster ${CLUSTER} -manyids -rmvdir -max_jobs ${MAX_JOBS} -makefile ${MAKE_PARA} -nouse_subdir -modelsdir ${TESTING}/${ALPHADIR} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult150-single-tr12.run' < networks/${DATASET}-single-${ARCHITECTURE}-tr12-${ALPHANAME}-mult50.nets
	${PARA_TRICKLE} -se2log -cluster ${CLUSTER} -manyids -rmvdir -max_jobs ${MAX_JOBS} -makefile ${MAKE_PARA} -nouse_subdir -modelsdir ${TESTING}/${ALPHADIR} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult150-single-tr23.run' < networks/${DATASET}-single-${ARCHITECTURE}-tr23-${ALPHANAME}-mult50.nets
	${PARA_TRICKLE} -se2log -cluster ${CLUSTER} -manyids -rmvdir -max_jobs ${MAX_JOBS} -makefile ${MAKE_PARA} -nouse_subdir -modelsdir ${TESTING}/${ALPHADIR} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult150-single-tr31.run' < networks/${DATASET}-single-${ARCHITECTURE}-tr31-${ALPHANAME}-mult50.nets

collect-single-mult150-data:
	../run-scripts/collect-data150 -txxalign single -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -data tr12 < networks/${DATASET}-single-${ARCHITECTURE}-tr12-${ALPHANAME}-mult50.nets > quality-reports/${DATASET}-single-${ARCHITECTURE}-tr12-mult150-${ALPHANAME}.rdb
	../run-scripts/collect-data150 -txxalign single -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -data tr23 < networks/${DATASET}-single-${ARCHITECTURE}-tr23-${ALPHANAME}-mult50.nets > quality-reports/${DATASET}-single-${ARCHITECTURE}-tr23-mult150-${ALPHANAME}.rdb
	../run-scripts/collect-data150 -txxalign single -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -data tr31 < networks/${DATASET}-single-${ARCHITECTURE}-tr31-${ALPHANAME}-mult50.nets > quality-reports/${DATASET}-single-${ARCHITECTURE}-tr31-mult150-${ALPHANAME}.rdb

trAB-single-mult250.scripts:
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult250-single-tr12.scripts' < networks/${DATASET}-single-${ARCHITECTURE}-tr12-${ALPHANAME}-mult150.nets
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult250-single-tr23.scripts' < networks/${DATASET}-single-${ARCHITECTURE}-tr23-${ALPHANAME}-mult150.nets
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult250-single-tr31.scripts' < networks/${DATASET}-single-${ARCHITECTURE}-tr31-${ALPHANAME}-mult150.nets

trAB-single-mult250.run:
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult250-single-tr12.run' < networks/${DATASET}-single-${ARCHITECTURE}-tr12-${ALPHANAME}-mult150.nets
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult250-single-tr23.run' < networks/${DATASET}-single-${ARCHITECTURE}-tr23-${ALPHANAME}-mult150.nets
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} mult250-single-tr31.run' < networks/${DATASET}-single-${ARCHITECTURE}-tr31-${ALPHANAME}-mult150.nets

collect-single-mult250-data:
	../run-scripts/collect-data250 -txxalign single -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -data tr12 < networks/${DATASET}-single-${ARCHITECTURE}-tr12-${ALPHANAME}-mult150.nets > quality-reports/${DATASET}-single-${ARCHITECTURE}-tr12-mult250-${ALPHANAME}.rdb
	../run-scripts/collect-data250 -txxalign single -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -data tr23 < networks/${DATASET}-single-${ARCHITECTURE}-tr23-${ALPHANAME}-mult150.nets > quality-reports/${DATASET}-single-${ARCHITECTURE}-tr23-mult250-${ALPHANAME}.rdb
	../run-scripts/collect-data250 -txxalign single -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} -data tr31 < networks/${DATASET}-single-${ARCHITECTURE}-tr31-${ALPHANAME}-mult150.nets > quality-reports/${DATASET}-single-${ARCHITECTURE}-tr31-mult250-${ALPHANAME}.rdb

trAB-single-test.scripts:
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} test-single-tr12.scripts' < networks/${DATASET}-single-${ARCHITECTURE}-tr12-${ALPHANAME}-mult250.nets
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} test-single-tr23.scripts' < networks/${DATASET}-single-${ARCHITECTURE}-tr23-${ALPHANAME}-mult250.nets
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} test-single-tr31.scripts' < networks/${DATASET}-single-${ARCHITECTURE}-tr31-${ALPHANAME}-mult250.nets

trAB-single-test.run:
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} test-single-tr12.run' < networks/${DATASET}-single-${ARCHITECTURE}-tr12-${ALPHANAME}-mult250.nets
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} test-single-tr23.run' < networks/${DATASET}-single-${ARCHITECTURE}-tr23-${ALPHANAME}-mult250.nets
	${DO_PARALLEL} -targets 'TXXALIGN=single ALPHANAME=${ALPHANAME} ALPHALIBFILE=${ALPHALIBFILE} ALPHADIR=${ALPHADIR}  ARCHITECTURE=${ARCHITECTURE} DATASET=${DATASET} test-single-tr31.run' < networks/${DATASET}-single-${ARCHITECTURE}-tr31-${ALPHANAME}-mult250.nets

collect-single-test-data:
	../run-scripts/collect-data-test -txxalign single -dataset ${DATASET} -arch ${ARCHITECTURE} -alphaname ${ALPHANAME} > quality-reports/${DATASET}-single-${ARCHITECTURE}-${ALPHANAME}-test.results

SEEDED-SCRIPT ?= run-scripts/${DATASET}-${ARCHITECTURE}-${ALPHANAME}-seeded.script
TRAINSET ?= tr12
ALIGN ?= t06

seeded.scripts:
	cat ../run-scripts/DATASET-ARCHITECTURE-ALPHANAME-seeded.template.script | \
          ${SUBST}  | \
          sed -e "s/TRAINSET/${TRAINSET}/" | \
          sed -e "s/DATASET/${DATASET}/" | \
          sed -e "s/ALIGN/${ALIGN}/" | \
          cat > ${SEEDED-SCRIPT}

seeded.run:
	${PARA_TRICKLE} -cluster ${CLUSTER} -rmvdir -quick '${PREDICT-2ND} < ${SEEDED-SCRIPT} >& logs/${DATASET}-${ARCHITECTURE}-seeded.log'