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246 lines
7.6 KiB
Makefile
246 lines
7.6 KiB
Makefile
#! /usr/local/bin/gmake
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# $Id: Makefile 15479 2016-10-10 16:25:21Z elilevy $
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# makfile for yaep5
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# use LOGREP=t or DOUBLEREP=t to activate logRep or doubleRep respectively (or setenv DOUBLEREP in the shell)
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#DOUBLEREP=t
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#LOGREP=t
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Libsources= AddLog.cpp NNiProp.cpp NNiSep.cpp Nni.cpp aaJC.cpp \
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allTrees.cpp allTreesSeparateModel.cpp alphabet.cpp amino.cpp \
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bestAlpha.cpp bestAlphaManyTrees.cpp bestHKYparam.cpp bootstrap.cpp \
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bblEM.cpp bblEMfixRoot.cpp bblEMProprtional.cpp bblEMProportionalEB.cpp bblLSProportionalEB.cpp bblEMSeperate.cpp \
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chebyshevAccelerator.cpp clustalFormat.cpp codon.cpp codonJC.cpp \
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computeCounts.cpp computeDownAlg.cpp computeMarginalAlg.cpp \
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computePijComponent.cpp computeUpAlg.cpp computeUpAlgFactors.cpp \
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computeSubstitutionCounts.cpp \
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computePosteriorExpectationOfSubstitutions.cpp \
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computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp \
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ConversionUtils.cpp countTableComponent.cpp datMatrixHolder.cpp distanceTable.cpp \
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distribution.cpp errorMsg.cpp evaluateCharacterFreq.cpp \
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fastStartTree.cpp fastaFormat.cpp findRateOfGene.cpp \
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fromCountTableComponentToDistance.cpp fromCountTableComponentToDistancefixRoot.cpp \
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fromCountTableComponentToDistanceProp.cpp fromCountTableComponentToDistancePropEB.cpp fromQtoPt.cpp \
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generalGammaDistributionFixedCategories.cpp gammaDistribution.cpp gammaUtilities.cpp \
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generalGammaDistribution.cpp getRandomWeights.cpp goldmanYangModel.cpp \
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granthamChemicalDistances.cpp hky.cpp simulateWithDependence.cpp KH_calculation.cpp likeDist.cpp likeDistfixRoot.cpp \
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likeDistProp.cpp likeDistPropEB.cpp likelihoodComputation.cpp \
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likelihoodComputationFactors.cpp logFile.cpp maseFormat.cpp \
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molphyFormat.cpp nexusFormat.cpp nj.cpp njConstrain.cpp \
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nucJC.cpp nucleotide.cpp numRec.cpp Parameters.cpp phylipFormat.cpp \
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pijAccelerator.cpp readDatMatrix.cpp readTree.cpp recognizeFormat.cpp \
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replacementModel.cpp searchStatus.cpp seqContainerTreeMap.cpp \
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sequence.cpp sequenceContainer.cpp simulateTree.cpp \
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siteSpecificRate.cpp someUtil.cpp split.cpp splitMap.cpp \
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splitTreeUtil.cpp stochasticProcess.cpp suffStatComponent.cpp \
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talRandom.cpp tree.cpp treeIt.cpp treeUtil.cpp uniDistribution.cpp \
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uniformDistribution.cpp cmdline2EvolObjs.cpp \
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generalGammaDistributionLaguerre.cpp gammaDistributionLaguerre.cpp GLaguer.cpp \
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givenRatesMLDistance.cpp distanceBasedSeqs2Tree.cpp \
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posteriorDistance.cpp pairwiseGammaDistance.cpp doubleRep.cpp \
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logRep.cpp indel.cpp indelModel.cpp mulAlphabet.cpp \
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replacementModelSSRV.cpp stochasticProcessSSRV.cpp bestAlphaAndNu.cpp \
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C_evalParamUSSRV.cpp matrixUtils.cpp betaOmegaDistribution.cpp \
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betaUtilities.cpp betaDistribution.cpp geneticCodeHolder.cpp \
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samplingSequences.cpp bblEM2USSRV.cpp bestParamUSSRV.cpp \
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likeDist2USSRV.cpp ussrvModel.cpp likelihoodComputation2USSRV.cpp \
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fromCountTableComponentToDistance2USSRV.cpp normalDist.cpp \
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tamura92.cpp bestTamura92param.cpp phylipSequentialFormat.cpp \
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simulateCodonsJumps.cpp \
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simulateJumpsAbstract.cpp \
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ssrvDistanceSeqs2Tree.cpp multipleStochasticProcess.cpp distributionPlusInvariant.cpp\
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extremeValDistribution.cpp \
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gammaDistributionFixedCategories.cpp generalGammaDistributionPlusInvariant.cpp gammaDistributionPlusInvariant.cpp \
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distributionPlusCategory.cpp simulateJumps.cpp computeJumps.cpp seqeuncesFilter.cpp \
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optGammaMixtureLS.cpp mixtureDistribution.cpp suffStatGammaMixture.cpp GamMixtureOptimizer.cpp optGammaMixtureEM.cpp gainLossAlphabet.cpp \
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wYangModel.cpp codonUtils.cpp likelihoodComputation2Codon.cpp likeDist2Codon.cpp unObservableData.cpp likelihoodComputationGL.cpp \
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threeStateModel.cpp threeStateAlphabet.cpp oneTwoMoreModel.cpp betaDistributionFixedCategories.cpp betaDistributionFixedCategoriesWithOmegaUniform.cpp \
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bblEM2codon.cpp bestAlphaAndK.cpp fromCountTableComponentToDistance2Codon.cpp\
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gtrModel.cpp bestGtrModelParams.cpp simulateRateShiftJumps.cpp integerAlphabet.cpp
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# do not use: fromInstructionFile.cpp, simulateSequnce.cpp split.save.cpp
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# LibCsources= cmdline.c
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# LibCsources += getopt.c getopt1.c
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EXEC =
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#TEST_EXEC_SUB = split_test splitMap_test bootstrap_test
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TEST_EXEC = $(addprefix tests/,$(TEST_EXEC_SUB))
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LIB = libEvolTree.a
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DEBUGLIB = $(LIB:.a=Debug.a)
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DOUBLEREPLIB = $(LIB:.a=DoubleRep.a)
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#CC=g++
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CXX=g++
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CC=$(CXX)
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#requres 2.13, but may work with 2.11
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GENGETOPT = gengetopt
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# osX/tiger
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#GENGETOPT = /opt/local/bin/gengetopt
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.SECONDARY: semphy_cmdline.c semphy_cmdline.h
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#LDFLAGS=
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CPPFLAGS= -O3 -Wall -Wno-sign-compare -I. -DLOG
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CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -DLOG -DVERBOS
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#CPPFLAGSDOU= $(CPPFLAGS)
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#-pg
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#CPPFLAGS+= -I/usr/include/g++-v3
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#CPPFLAGS+= -DLOG -DLOGCLS -DMEMCHK
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# sources
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sources= $(Libsources) $(LibCsources) $(addsuffix .cpp,$(EXEC) $(TEST_EXEC))
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.PHONY: tests lib test debug %.debug
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.PHONY: dat DOUBLEREP doubleRep
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all: lib $(EXEC)
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test: all tests
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+cd tests; make -k test
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ifdef DOUBLEREP
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CPPFLAGS+= -DLOGREP
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CPPFLAGSDEBUG += -DLOGREP
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LDFLAGSDEBUG += -DLOGREP
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endif
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#ifdef DOUBLEREP
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#CPPFLAGS+= -DDOUBLEREP
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#CPPFLAGSDEBUG += -DDOUBLEREP
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#LDFLAGSDEBUG += -DDOUBLEREP
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#endif
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debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG
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debug: $(DEBUGLIB)
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pl:
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@echo "lib ="$(LIB)
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@echo "debug="$(DEBUGLIB)
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#debug: all
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# cp libEvolTree.a libEvolTreeDebug.a
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# <<<<<<< Makefile
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# %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-25
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# % debug: LIB = libEvolTreeDebug.a
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# %.debug: %
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# @echo "made \""$(*)"\" in debug mode"
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# =======
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#>>>>>>> 2.34
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lib: $(LIB)
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$(LIB): $(Libsources:.cpp=.o) $(LibCsources:.c=.o)
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ar rv $@ $?
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ranlib $@
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tags: *.cpp *.h
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etags --members --language=c++ $^
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$(EXEC) $(TEST_EXEC): $(LIB)
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tests: $(TEST_EXEC)
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-include make.dep
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install:
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cd ../fast; make -f Makefile.lib install_do
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clean:
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-rm -f $(LIB) $(DEBUGLIB) $(DOUBLEREPLIB) $(EXEC) $(TEST_EXEC) *.o
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ifneq ($(wildcard make.dep), make.dep)
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make.dep: depend
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endif
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depend makedep: _make.dep
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@mv -f _make.dep make.dep
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_make.dep: $(sources)
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@echo making depend
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# $(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@ ; [ -s $@ ] || rm -f $@'
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@$(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ | sed "s/\(^[^.]*\)\.o/\1.o \1.debug.o/g" > $@'
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_fast:
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cd ../fast;make -f Makefile.lib -k all
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fast.% _fast.%:
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cd ../fast;make -f Makefile.lib -k $(*)
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simulateSequnce: simulateSequnce_cmdline.o
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evolObjsTest.ggo: evolObjs.header evolObjs.args
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cat $^ > $@
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# commandline (gengetopts)
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%_cmdline.h %_cmdline.c: %.ggo
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$(GENGETOPT) -i$< -F$(*)_cmdline
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%.dat.q: %.dat
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awk 'BEGIN{RS="[\n\r]+";};{print "\" "$$0" \"\r"}' $< > $@
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# cat $@
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DAT = cpREV45.dat.q dayhoff.dat.q jones.dat.q mtREV24.dat.q wag.dat.q HIVb.dat.q HIVw.dat.q
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dat: $(DAT)
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cleandat:
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rm $(DAT)
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datMatrixHolder.o: $(DAT)
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.PRECIOUS: $(DAT)
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debug: LIB = $(DEBUGLIB)
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%.debug: CPPFLAGS = $(CPPFLAGSDEBUG)
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%.debug: %
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@echo "made \""$(*)"\" in debug mode"
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%.debug.o: %.c
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$(CC) -c $(CPPFLAGSDEBUG) $(CFLAGS) $< -o $@
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%.debug.o: %.cpp
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$(CXX) -c $(CPPFLAGSDEBUG) $(CXXFLAGS) $< -o $@
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$(DEBUGLIB): $(Libsources:.cpp=.debug.o) $(LibCsources:.c=.debug.o)
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ar rv $@ $?
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ranlib $@
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doubleRep: LOGREP=t
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doubleRep: CPPFLAGS+= -DLOGREP
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#doubleRep: DOUBLEREP=t
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#doubleRep: CPPFLAGS+= -DDOUBLEREP
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doubleRep: $(DOUBLEREPLIB)
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%.doubleRep.o: %.c
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$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@
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%.doubleRep.o: %.cpp
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$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@
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$(DOUBLEREPLIB): $(Libsources:.cpp=.doubleRep.o) $(LibCsources:.c=.doubleRep.o)
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ar rv $@ $?
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ranlib $@
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# DO NOT DELETE
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