-###################################################\r
-#\r
-# Makefile for mothur\r
-# Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]\r
-# Created: April 16, 2010\r
-#\r
-###################################################\r
-\r
-#\r
-# Macros\r
-#\r
-\r
-CC = g++ \r
-CC_OPTIONS = -O3\r
-\r
-# if you do not want to use the readline library set to no, default yes.\r
-# make sure you have the library installed\r
-\r
-USEREADLINE ?= yes\r
-\r
-ifeq ($(strip $(USEREADLINE)),yes)\r
- CC_OPTIONS += -DUSE_READLINE\r
- LNK_OPTIONS += \\r
- -lreadline\\r
- -lncurses\\r
- -L../readline-6.0\r
-endif\r
-\r
-USEMPI ?= no\r
-\r
-ifeq ($(strip $(USEMPI)),yes)\r
- CC = mpic++\r
- CC_OPTIONS += -DUSE_MPI\r
-endif\r
-\r
-#\r
-# INCLUDE directories for mothur\r
-#\r
-\r
- INCLUDE = -I.\r
-\r
-#\r
-# Build mothur\r
-#\r
-\r
-mothur : \\r
- ./sharedutilities.o\\r
- ./treegroupscommand.o\\r
- ./bootstrapsharedcommand.o\\r
- ./matrixoutputcommand.o\\r
- ./getoturepcommand.o\\r
- ./screenseqscommand.o\\r
- ./chimera.o\\r
- ./decalc.o\\r
- ./readotucommand.o\\r
- ./readdistcommand.o\\r
- ./commandfactory.o\\r
- ./alignment.o\\r
- ./alignmentcell.o\\r
- ./gotohoverlap.o\\r
- ./overlap.o\\r
- ./needlemanoverlap.o\\r
- ./blastalign.o\\r
- ./noalign.o\\r
- ./suffixdb.o\\r
- ./suffixnodes.o\\r
- ./suffixtree.o\\r
- ./blastdb.o\\r
- ./nast.o\\r
- ./nastreport.o\\r
- ./boneh.o\\r
- ./efron.o\\r
- ./solow.o\\r
- ./unifracweightedcommand.o\\r
- ./weighted.o\\r
- ./unweighted.o\\r
- ./unifracunweightedcommand.o\\r
- ./getsabundcommand.o\\r
- ./getrabundcommand.o\\r
- ./bellerophon.o\\r
- ./pintail.o\\r
- ./sharedanderbergs.o\\r
- ./venncommand.o\\r
- ./venn.o\\r
- ./fullmatrix.o\\r
- ./heatmap.o\\r
- ./heatmapcommand.o\\r
- ./libshuffcommand.o\\r
- ./nocommands.o\\r
- ./sharedbraycurtis.o\\r
- ./sharedkulczynski.o\\r
- ./sharedlennon.o\\r
- ./sharedkulczynskicody.o\\r
- ./sharedmorisitahorn.o\\r
- ./sharedochiai.o\\r
- ./readcolumn.o\\r
- ./readotu.o\\r
- ./readphylip.o\\r
- ./consensuscommand.o\\r
- ./heatmapsimcommand.o\\r
- ./heatmapsim.o\\r
- ./optionparser.o\\r
- ./filterseqscommand.o\\r
- ./goodscoverage.o\\r
- ./sequencedb.o\\r
- ./sharedjackknife.o\\r
- ./sharedmarczewski.o\\r
- ./aligncommand.o\\r
- ./treemap.o\\r
- ./parsimonycommand.o\\r
- ./parsimony.o\\r
- ./seqsummarycommand.o\\r
- ./chimeraccodecommand.o\\r
- ./chimerabellerophoncommand.o\\r
- ./chimeracheckcommand.o\\r
- ./chimeraslayercommand.o\\r
- ./chimerapintailcommand.o\\r
- ./chimeraseqscommand.o\\r
- ./sharedlistvector.o\\r
- ./tree.o\\r
- ./readtree.o\\r
- ./sharedsobscollectsummary.o\\r
- ./deconvolutecommand.o\\r
- ./listseqscommand.o\\r
- ./getseqscommand.o\\r
- ./removeseqscommand.o\\r
- ./systemcommand.o\\r
- ./binsequencecommand.o\\r
- ./distancecommand.o\\r
- ./ace.o\\r
- ./averagelinkage.o\\r
- ./bootstrap.o\\r
- ./calculator.o\\r
- ./chao1.o\\r
- ./cluster.o\\r
- ./clustercommand.o\\r
- ./collect.o\\r
- ./collectcommand.o\\r
- ./collectsharedcommand.o\\r
- ./commandoptionparser.o\\r
- ./completelinkage.o\\r
- ./database.o\\r
- ./engine.o\\r
- ./fastamap.o\\r
- ./fileoutput.o\\r
- ./globaldata.o\\r
- ./groupmap.o\\r
- ./helpcommand.o\\r
- ./makegroupcommand.o\\r
- ./chopseqscommand.o\\r
- ./clearcutcommand.o\\r
- ./catchallcommand.o\\r
- ./splitabundcommand.o\\r
- ./splitmatrix.o\\r
- ./clustersplitcommand.o\\r
- ./weightedlinkage.o\\r
- ./inputdata.o\\r
- ./jackknife.o\\r
- ./kmer.o\\r
- ./kmerdb.o\\r
- ./listvector.o\\r
- ./mothur.o\\r
- ./nameassignment.o\\r
- ./npshannon.o\\r
- ./ordervector.o\\r
- ./progress.o\\r
- ./quitcommand.o\\r
- ./rabundvector.o\\r
- ./rarecalc.o\\r
- ./raredisplay.o\\r
- ./rarefact.o\\r
- ./rarefactcommand.o\\r
- ./rarefactsharedcommand.o\\r
- ./sabundvector.o\\r
- ./sequence.o\\r
- ./shannon.o\\r
- ./sharedace.o\\r
- ./sharedchao1.o\\r
- ./sharedcommand.o\\r
- ./sharedjabund.o\\r
- ./sharedjclass.o\\r
- ./sharedjest.o\\r
- ./sharedordervector.o\\r
- ./sharedrabundvector.o\\r
- ./sharedsabundvector.o\\r
- ./sharedsobs.o\\r
- ./sharedsorabund.o\\r
- ./sharedsorclass.o\\r
- ./sharedsorest.o\\r
- ./sharedthetan.o\\r
- ./sharedthetayc.o\\r
- ./simpson.o\\r
- ./singlelinkage.o\\r
- ./sparsematrix.o\\r
- ./summarycommand.o\\r
- ./summarysharedcommand.o\\r
- ./uvest.o\\r
- ./validcalculator.o\\r
- ./validparameter.o\\r
- ./treenode.o\\r
- ./readtreecommand.o\\r
- ./reversecommand.o\\r
- ./trimseqscommand.o\\r
- ./slibshuff.o\\r
- ./libshuff.o\\r
- ./dlibshuff.o\\r
- ./mergefilecommand.o\\r
- ./coverage.o\\r
- ./whittaker.o\\r
- ./preclustercommand.o\\r
- ./otuhierarchycommand.o\\r
- ./setdircommand.o\\r
- ./getgroupcommand.o\\r
- ./getlabelcommand.o\\r
- ./secondarystructurecommand.o\\r
- ./mothurout.o\\r
- ./parselistscommand.o\\r
- ./readblast.o\\r
- ./chimeracheckrdp.o\\r
- ./hclustercommand.o\\r
- ./hcluster.o\\r
- ./getlistcountcommand.o\\r
- ./readcluster.o\\r
- ./ccode.o\\r
- ./taxonomyequalizer.o\\r
- ./phylotypecommand.o\\r
- ./classifyseqscommand.o\\r
- ./classifyotucommand.o\\r
- ./parsesffcommand.o\\r
- ./classify.o\\r
- ./phylotree.o\\r
- ./phylodiversity.o\\r
- ./phylodiversitycommand.o\\r
- ./bayesian.o\\r
- ./phylosummary.o\\r
- ./alignmentdb.o\\r
- ./knn.o\\r
- ./distancedb.o\\r
- ./chimeraslayer.o\\r
- ./slayer.o\\r
- ./pcacommand.o\\r
- ./formatcolumn.o\\r
- ./formatphylip.o\\r
- ./mgclustercommand.o\\r
- ./getsharedotucommand.o\\r
- ./maligner.o\\r
- ./chimerarealigner.o\\r
- ./bergerparker.o\\r
- ./bstick.o\\r
- ./sharedkstest.o\\r
- ./qstat.o\\r
- ./shen.o\\r
- ./logsd.o\\r
- ./geom.o\\r
- ./setlogfilecommand.o\r
- $(CC) $(LNK_OPTIONS) \\r
- ./sharedutilities.o\\r
- ./treegroupscommand.o\\r
- ./bootstrapsharedcommand.o\\r
- ./matrixoutputcommand.o\\r
- ./getoturepcommand.o\\r
- ./screenseqscommand.o\\r
- ./chimera.o\\r
- ./decalc.o\\r
- ./readotucommand.o\\r
- ./readdistcommand.o\\r
- ./commandfactory.o\\r
- ./alignment.o\\r
- ./alignmentcell.o\\r
- ./gotohoverlap.o\\r
- ./overlap.o\\r
- ./needlemanoverlap.o\\r
- ./blastalign.o\\r
- ./noalign.o\\r
- ./suffixdb.o\\r
- ./suffixnodes.o\\r
- ./suffixtree.o\\r
- ./blastdb.o\\r
- ./nast.o\\r
- ./nastreport.o\\r
- ./boneh.o\\r
- ./efron.o\\r
- ./solow.o\\r
- ./unifracweightedcommand.o\\r
- ./weighted.o\\r
- ./unweighted.o\\r
- ./unifracunweightedcommand.o\\r
- ./getsabundcommand.o\\r
- ./getrabundcommand.o\\r
- ./bellerophon.o\\r
- ./pintail.o\\r
- ./sharedanderbergs.o\\r
- ./venncommand.o\\r
- ./venn.o\\r
- ./fullmatrix.o\\r
- ./heatmap.o\\r
- ./heatmapcommand.o\\r
- ./libshuffcommand.o\\r
- ./nocommands.o\\r
- ./sharedbraycurtis.o\\r
- ./sharedkulczynski.o\\r
- ./sharedlennon.o\\r
- ./sharedkulczynskicody.o\\r
- ./sharedmorisitahorn.o\\r
- ./sharedochiai.o\\r
- ./readcolumn.o\\r
- ./readotu.o\\r
- ./readphylip.o\\r
- ./consensuscommand.o\\r
- ./heatmapsimcommand.o\\r
- ./heatmapsim.o\\r
- ./optionparser.o\\r
- ./filterseqscommand.o\\r
- ./goodscoverage.o\\r
- ./sequencedb.o\\r
- ./sharedjackknife.o\\r
- ./sharedmarczewski.o\\r
- ./aligncommand.o\\r
- ./treemap.o\\r
- ./parsimonycommand.o\\r
- ./parsimony.o\\r
- ./seqsummarycommand.o\\r
- ./chimeraccodecommand.o\\r
- ./chimerabellerophoncommand.o\\r
- ./chimeracheckcommand.o\\r
- ./chimeraslayercommand.o\\r
- ./chimerapintailcommand.o\\r
- ./chimeraseqscommand.o\\r
- ./sharedlistvector.o\\r
- ./tree.o\\r
- ./readtree.o\\r
- ./sharedsobscollectsummary.o\\r
- ./deconvolutecommand.o\\r
- ./listseqscommand.o\\r
- ./getseqscommand.o\\r
- ./removeseqscommand.o\\r
- ./systemcommand.o\\r
- ./binsequencecommand.o\\r
- ./distancecommand.o\\r
- ./ace.o\\r
- ./averagelinkage.o\\r
- ./bootstrap.o\\r
- ./calculator.o\\r
- ./chao1.o\\r
- ./cluster.o\\r
- ./clustercommand.o\\r
- ./collect.o\\r
- ./collectcommand.o\\r
- ./collectsharedcommand.o\\r
- ./commandoptionparser.o\\r
- ./completelinkage.o\\r
- ./database.o\\r
- ./engine.o\\r
- ./fastamap.o\\r
- ./fileoutput.o\\r
- ./globaldata.o\\r
- ./groupmap.o\\r
- ./helpcommand.o\\r
- ./makegroupcommand.o\\r
- ./chopseqscommand.o\\r
- ./clearcutcommand.o\\r
- ./catchallcommand.o\\r
- ./splitabundcommand.o\\r
- ./splitmatrix.o\\r
- ./clustersplitcommand.o\\r
- ./weightedlinkage.o\\r
- ./inputdata.o\\r
- ./jackknife.o\\r
- ./kmer.o\\r
- ./kmerdb.o\\r
- ./listvector.o\\r
- ./mothur.o\\r
- ./nameassignment.o\\r
- ./npshannon.o\\r
- ./ordervector.o\\r
- ./progress.o\\r
- ./quitcommand.o\\r
- ./rabundvector.o\\r
- ./rarecalc.o\\r
- ./raredisplay.o\\r
- ./rarefact.o\\r
- ./rarefactcommand.o\\r
- ./rarefactsharedcommand.o\\r
- ./sabundvector.o\\r
- ./sequence.o\\r
- ./shannon.o\\r
- ./sharedace.o\\r
- ./sharedchao1.o\\r
- ./sharedcommand.o\\r
- ./sharedjabund.o\\r
- ./sharedjclass.o\\r
- ./sharedjest.o\\r
- ./sharedordervector.o\\r
- ./sharedrabundvector.o\\r
- ./sharedsabundvector.o\\r
- ./sharedsobs.o\\r
- ./sharedsorabund.o\\r
- ./sharedsorclass.o\\r
- ./sharedsorest.o\\r
- ./sharedthetan.o\\r
- ./sharedthetayc.o\\r
- ./simpson.o\\r
- ./singlelinkage.o\\r
- ./sparsematrix.o\\r
- ./summarycommand.o\\r
- ./summarysharedcommand.o\\r
- ./uvest.o\\r
- ./validcalculator.o\\r
- ./validparameter.o\\r
- ./treenode.o\\r
- ./readtreecommand.o\\r
- ./reversecommand.o\\r
- ./trimseqscommand.o\\r
- ./slibshuff.o\\r
- ./libshuff.o\\r
- ./dlibshuff.o\\r
- ./mergefilecommand.o\\r
- ./coverage.o\\r
- ./whittaker.o\\r
- ./preclustercommand.o\\r
- ./otuhierarchycommand.o\\r
- ./setdircommand.o\\r
- ./getgroupcommand.o\\r
- ./getlabelcommand.o\\r
- ./secondarystructurecommand.o\\r
- ./mothurout.o\\r
- ./parselistscommand.o\\r
- ./readblast.o\\r
- ./chimeracheckrdp.o\\r
- ./hclustercommand.o\\r
- ./hcluster.o\\r
- ./getlistcountcommand.o\\r
- ./readcluster.o\\r
- ./ccode.o\\r
- ./taxonomyequalizer.o\\r
- ./phylotypecommand.o\\r
- ./classifyseqscommand.o\\r
- ./classifyotucommand.o\\r
- ./parsesffcommand.o\\r
- ./classify.o\\r
- ./phylotree.o\\r
- ./phylodiversity.o\\r
- ./phylodiversitycommand.o\\r
- ./bayesian.o\\r
- ./phylosummary.o\\r
- ./alignmentdb.o\\r
- ./knn.o\\r
- ./distancedb.o\\r
- ./chimeraslayer.o\\r
- ./slayer.o\\r
- ./pcacommand.o\\r
- ./formatcolumn.o\\r
- ./formatphylip.o\\r
- ./mgclustercommand.o\\r
- ./getsharedotucommand.o\\r
- ./maligner.o\\r
- ./chimerarealigner.o\\r
- ./bergerparker.o\\r
- ./bstick.o\\r
- ./sharedkstest.o\\r
- ./qstat.o\\r
- ./shen.o\\r
- ./logsd.o\\r
- ./geom.o\\r
- ./setlogfilecommand.o\\r
- -o mothur\r
-\r
-clean : \r
- rm \\r
- ./sharedutilities.o\\r
- ./treegroupscommand.o\\r
- ./bootstrapsharedcommand.o\\r
- ./matrixoutputcommand.o\\r
- ./getoturepcommand.o\\r
- ./screenseqscommand.o\\r
- ./chimera.o\\r
- ./decalc.o\\r
- ./readotucommand.o\\r
- ./readdistcommand.o\\r
- ./commandfactory.o\\r
- ./alignment.o\\r
- ./alignmentcell.o\\r
- ./gotohoverlap.o\\r
- ./overlap.o\\r
- ./needlemanoverlap.o\\r
- ./blastalign.o\\r
- ./noalign.o\\r
- ./suffixdb.o\\r
- ./suffixnodes.o\\r
- ./suffixtree.o\\r
- ./blastdb.o\\r
- ./nast.o\\r
- ./nastreport.o\\r
- ./boneh.o\\r
- ./efron.o\\r
- ./solow.o\\r
- ./unifracweightedcommand.o\\r
- ./weighted.o\\r
- ./unweighted.o\\r
- ./unifracunweightedcommand.o\\r
- ./getsabundcommand.o\\r
- ./getrabundcommand.o\\r
- ./bellerophon.o\\r
- ./pintail.o\\r
- ./sharedanderbergs.o\\r
- ./venncommand.o\\r
- ./venn.o\\r
- ./fullmatrix.o\\r
- ./heatmap.o\\r
- ./heatmapcommand.o\\r
- ./libshuffcommand.o\\r
- ./nocommands.o\\r
- ./sharedbraycurtis.o\\r
- ./sharedkulczynski.o\\r
- ./sharedlennon.o\\r
- ./sharedkulczynskicody.o\\r
- ./sharedmorisitahorn.o\\r
- ./sharedochiai.o\\r
- ./readcolumn.o\\r
- ./readotu.o\\r
- ./readphylip.o\\r
- ./consensuscommand.o\\r
- ./heatmapsimcommand.o\\r
- ./heatmapsim.o\\r
- ./optionparser.o\\r
- ./filterseqscommand.o\\r
- ./goodscoverage.o\\r
- ./sequencedb.o\\r
- ./sharedjackknife.o\\r
- ./sharedmarczewski.o\\r
- ./aligncommand.o\\r
- ./treemap.o\\r
- ./parsimonycommand.o\\r
- ./parsimony.o\\r
- ./seqsummarycommand.o\\r
- ./chimeraccodecommand.o\\r
- ./chimerabellerophoncommand.o\\r
- ./chimeracheckcommand.o\\r
- ./chimeraslayercommand.o\\r
- ./chimerapintailcommand.o\\r
- ./chimeraseqscommand.o\\r
- ./sharedlistvector.o\\r
- ./tree.o\\r
- ./readtree.o\\r
- ./sharedsobscollectsummary.o\\r
- ./deconvolutecommand.o\\r
- ./listseqscommand.o\\r
- ./getseqscommand.o\\r
- ./removeseqscommand.o\\r
- ./systemcommand.o\\r
- ./binsequencecommand.o\\r
- ./distancecommand.o\\r
- ./ace.o\\r
- ./averagelinkage.o\\r
- ./bootstrap.o\\r
- ./calculator.o\\r
- ./chao1.o\\r
- ./cluster.o\\r
- ./clustercommand.o\\r
- ./collect.o\\r
- ./collectcommand.o\\r
- ./collectsharedcommand.o\\r
- ./commandoptionparser.o\\r
- ./completelinkage.o\\r
- ./database.o\\r
- ./engine.o\\r
- ./fastamap.o\\r
- ./fileoutput.o\\r
- ./globaldata.o\\r
- ./groupmap.o\\r
- ./helpcommand.o\\r
- ./makegroupcommand.o\\r
- ./chopseqscommand.o\\r
- ./clearcutcommand.o\\r
- ./catchallcommand.o\\r
- ./splitabundcommand.o\\r
- ./splitmatrix.o\\r
- ./clustersplitcommand.o\\r
- ./weightedlinkage.o\\r
- ./inputdata.o\\r
- ./jackknife.o\\r
- ./kmer.o\\r
- ./kmerdb.o\\r
- ./listvector.o\\r
- ./mothur.o\\r
- ./nameassignment.o\\r
- ./npshannon.o\\r
- ./ordervector.o\\r
- ./progress.o\\r
- ./quitcommand.o\\r
- ./rabundvector.o\\r
- ./rarecalc.o\\r
- ./raredisplay.o\\r
- ./rarefact.o\\r
- ./rarefactcommand.o\\r
- ./rarefactsharedcommand.o\\r
- ./sabundvector.o\\r
- ./sequence.o\\r
- ./shannon.o\\r
- ./sharedace.o\\r
- ./sharedchao1.o\\r
- ./sharedcommand.o\\r
- ./sharedjabund.o\\r
- ./sharedjclass.o\\r
- ./sharedjest.o\\r
- ./sharedordervector.o\\r
- ./sharedrabundvector.o\\r
- ./sharedsabundvector.o\\r
- ./sharedsobs.o\\r
- ./sharedsorabund.o\\r
- ./sharedsorclass.o\\r
- ./sharedsorest.o\\r
- ./sharedthetan.o\\r
- ./sharedthetayc.o\\r
- ./simpson.o\\r
- ./singlelinkage.o\\r
- ./sparsematrix.o\\r
- ./summarycommand.o\\r
- ./summarysharedcommand.o\\r
- ./uvest.o\\r
- ./validcalculator.o\\r
- ./validparameter.o\\r
- ./treenode.o\\r
- ./readtreecommand.o\\r
- ./reversecommand.o\\r
- ./trimseqscommand.o\\r
- ./slibshuff.o\\r
- ./libshuff.o\\r
- ./dlibshuff.o\\r
- ./mergefilecommand.o\\r
- ./coverage.o\\r
- ./whittaker.o\\r
- ./preclustercommand.o\\r
- ./otuhierarchycommand.o\\r
- ./setdircommand.o\\r
- ./getgroupcommand.o\\r
- ./getlabelcommand.o\\r
- ./secondarystructurecommand.o\\r
- ./mothurout.o\\r
- ./parselistscommand.o\\r
- ./readblast.o\\r
- ./chimeracheckrdp.o\\r
- ./hclustercommand.o\\r
- ./hcluster.o\\r
- ./getlistcountcommand.o\\r
- ./readcluster.o\\r
- ./ccode.o\\r
- ./taxonomyequalizer.o\\r
- ./phylotypecommand.o\\r
- ./classifyseqscommand.o\\r
- ./classifyotucommand.o\\r
- ./parsesffcommand.o\\r
- ./classify.o\\r
- ./phylotree.o\\r
- ./phylodiversity.o\\r
- ./phylodiversitycommand.o\\r
- ./bayesian.o\\r
- ./phylosummary.o\\r
- ./alignmentdb.o\\r
- ./knn.o\\r
- ./distancedb.o\\r
- ./chimeraslayer.o\\r
- ./slayer.o\\r
- ./pcacommand.o\\r
- ./formatcolumn.o\\r
- ./formatphylip.o\\r
- ./mgclustercommand.o\\r
- ./getsharedotucommand.o\\r
- ./maligner.o\\r
- ./chimerarealigner.o\\r
- ./bergerparker.o\\r
- ./bstick.o\\r
- ./sharedkstest.o\\r
- ./qstat.o\\r
- ./shen.o\\r
- ./logsd.o\\r
- ./geom.o\\r
- ./setlogfilecommand.o\\r
- mothur\r
-\r
-install : mothur\r
- #cp mothur ../Release/mothur\r
-\r
-#\r
-# Build the parts of mothur\r
-#\r
-\r
-\r
-# Item # 1 -- sharedutilities --\r
-./sharedutilities.o : sharedutilities.cpp\r
- $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o\r
-\r
-\r
-# Item # 2 -- treegroupscommand --\r
-./treegroupscommand.o : treegroupscommand.cpp\r
- $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o\r
-\r
-\r
-# Item # 3 -- bootstrapsharedcommand --\r
-./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp\r
- $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o\r
-\r
-\r
-# Item # 4 -- matrixoutputcommand --\r
-./matrixoutputcommand.o : matrixoutputcommand.cpp\r
- $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o\r
-\r
-\r
-# Item # 5 -- getoturepcommand --\r
-./getoturepcommand.o : getoturepcommand.cpp\r
- $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o\r
-\r
-\r
-# Item # 6 -- screenseqscommand --\r
-./screenseqscommand.o : screenseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o\r
-\r
-\r
-# Item # 7 -- chimera --\r
-./chimera.o : chimera.cpp\r
- $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o\r
-\r
-\r
-# Item # 8 -- decalc --\r
-./decalc.o : decalc.cpp\r
- $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o\r
-\r
-\r
-# Item # 9 -- readotucommand --\r
-./readotucommand.o : readotucommand.cpp\r
- $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o\r
-\r
-\r
-# Item # 10 -- readdistcommand --\r
-./readdistcommand.o : readdistcommand.cpp\r
- $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o\r
-\r
-\r
-# Item # 11 -- commandfactory --\r
-./commandfactory.o : commandfactory.cpp\r
- $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o\r
-\r
-\r
-# Item # 12 -- alignment --\r
-./alignment.o : alignment.cpp\r
- $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o\r
-\r
-\r
-# Item # 13 -- alignmentcell --\r
-./alignmentcell.o : alignmentcell.cpp\r
- $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o\r
-\r
-\r
-# Item # 14 -- gotohoverlap --\r
-./gotohoverlap.o : gotohoverlap.cpp\r
- $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o\r
-\r
-\r
-# Item # 15 -- overlap --\r
-./overlap.o : overlap.cpp\r
- $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o\r
-\r
-\r
-# Item # 16 -- needlemanoverlap --\r
-./needlemanoverlap.o : needlemanoverlap.cpp\r
- $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o\r
-\r
-\r
-# Item # 17 -- blastalign --\r
-./blastalign.o : blastalign.cpp\r
- $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o\r
-\r
-\r
-# Item # 18 -- noalign --\r
-./noalign.o : noalign.cpp\r
- $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o\r
-\r
-\r
-# Item # 19 -- suffixdb --\r
-./suffixdb.o : suffixdb.cpp\r
- $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o\r
-\r
-\r
-# Item # 20 -- suffixnodes --\r
-./suffixnodes.o : suffixnodes.cpp\r
- $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o\r
-\r
-\r
-# Item # 21 -- suffixtree --\r
-./suffixtree.o : suffixtree.cpp\r
- $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o\r
-\r
-\r
-# Item # 22 -- blastdb --\r
-./blastdb.o : blastdb.cpp\r
- $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o\r
-\r
-\r
-# Item # 23 -- nast --\r
-./nast.o : nast.cpp\r
- $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o\r
-\r
-\r
-# Item # 24 -- nastreport --\r
-./nastreport.o : nastreport.cpp\r
- $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o\r
-\r
-\r
-# Item # 25 -- boneh --\r
-./boneh.o : boneh.cpp\r
- $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o\r
-\r
-\r
-# Item # 26 -- efron --\r
-./efron.o : efron.cpp\r
- $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o\r
-\r
-\r
-# Item # 27 -- solow --\r
-./solow.o : solow.cpp\r
- $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o\r
-\r
-\r
-# Item # 28 -- unifracweightedcommand --\r
-./unifracweightedcommand.o : unifracweightedcommand.cpp\r
- $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o\r
-\r
-\r
-# Item # 29 -- weighted --\r
-./weighted.o : weighted.cpp\r
- $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o\r
-\r
-\r
-# Item # 30 -- unweighted --\r
-./unweighted.o : unweighted.cpp\r
- $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o\r
-\r
-\r
-# Item # 31 -- unifracunweightedcommand --\r
-./unifracunweightedcommand.o : unifracunweightedcommand.cpp\r
- $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o\r
-\r
-\r
-# Item # 32 -- getsabundcommand --\r
-./getsabundcommand.o : getsabundcommand.cpp\r
- $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o\r
-\r
-\r
-# Item # 33 -- getrabundcommand --\r
-./getrabundcommand.o : getrabundcommand.cpp\r
- $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o\r
-\r
-\r
-# Item # 34 -- bellerophon --\r
-./bellerophon.o : bellerophon.cpp\r
- $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o\r
-\r
-\r
-# Item # 35 -- pintail --\r
-./pintail.o : pintail.cpp\r
- $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o\r
-\r
-\r
-# Item # 36 -- sharedanderbergs --\r
-./sharedanderbergs.o : sharedanderbergs.cpp\r
- $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o\r
-\r
-\r
-# Item # 37 -- venncommand --\r
-./venncommand.o : venncommand.cpp\r
- $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o\r
-\r
-\r
-# Item # 38 -- venn --\r
-./venn.o : venn.cpp\r
- $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o\r
-\r
-\r
-# Item # 39 -- fullmatrix --\r
-./fullmatrix.o : fullmatrix.cpp\r
- $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o\r
-\r
-\r
-# Item # 40 -- heatmap --\r
-./heatmap.o : heatmap.cpp\r
- $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o\r
-\r
-\r
-# Item # 41 -- heatmapcommand --\r
-./heatmapcommand.o : heatmapcommand.cpp\r
- $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o\r
-\r
-\r
-# Item # 42 -- libshuffcommand --\r
-./libshuffcommand.o : libshuffcommand.cpp\r
- $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o\r
-\r
-\r
-# Item # 43 -- nocommands --\r
-./nocommands.o : nocommands.cpp\r
- $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o\r
-\r
-\r
-# Item # 44 -- sharedbraycurtis --\r
-./sharedbraycurtis.o : sharedbraycurtis.cpp\r
- $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o\r
-\r
-\r
-# Item # 45 -- sharedkulczynski --\r
-./sharedkulczynski.o : sharedkulczynski.cpp\r
- $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o\r
-\r
-\r
-# Item # 46 -- sharedlennon --\r
-./sharedlennon.o : sharedlennon.cpp\r
- $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o\r
-\r
-\r
-# Item # 47 -- sharedkulczynskicody --\r
-./sharedkulczynskicody.o : sharedkulczynskicody.cpp\r
- $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o\r
-\r
-\r
-# Item # 48 -- sharedmorisitahorn --\r
-./sharedmorisitahorn.o : sharedmorisitahorn.cpp\r
- $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o\r
-\r
-\r
-# Item # 49 -- sharedochiai --\r
-./sharedochiai.o : sharedochiai.cpp\r
- $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o\r
-\r
-\r
-# Item # 50 -- readcolumn --\r
-./readcolumn.o : readcolumn.cpp\r
- $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o\r
-\r
-\r
-# Item # 51 -- readotu --\r
-./readotu.o : readotu.cpp\r
- $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o\r
-\r
-\r
-# Item # 52 -- readphylip --\r
-./readphylip.o : readphylip.cpp\r
- $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o\r
-\r
-\r
-# Item # 53 -- consensuscommand --\r
-./consensuscommand.o : consensuscommand.cpp\r
- $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o\r
-\r
-\r
-# Item # 54 -- heatmapsimcommand --\r
-./heatmapsimcommand.o : heatmapsimcommand.cpp\r
- $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o\r
-\r
-\r
-# Item # 55 -- heatmapsim --\r
-./heatmapsim.o : heatmapsim.cpp\r
- $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o\r
-\r
-\r
-# Item # 56 -- optionparser --\r
-./optionparser.o : optionparser.cpp\r
- $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o\r
-\r
-\r
-# Item # 57 -- filterseqscommand --\r
-./filterseqscommand.o : filterseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o\r
-\r
-\r
-# Item # 58 -- goodscoverage --\r
-./goodscoverage.o : goodscoverage.cpp\r
- $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o\r
-\r
-\r
-# Item # 59 -- sequencedb --\r
-./sequencedb.o : sequencedb.cpp\r
- $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o\r
-\r
-\r
-# Item # 60 -- sharedjackknife --\r
-./sharedjackknife.o : sharedjackknife.cpp\r
- $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o\r
-\r
-\r
-# Item # 61 -- sharedmarczewski --\r
-./sharedmarczewski.o : sharedmarczewski.cpp\r
- $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o\r
-\r
-\r
-# Item # 62 -- aligncommand --\r
-./aligncommand.o : aligncommand.cpp\r
- $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o\r
-\r
-\r
-# Item # 63 -- treemap --\r
-./treemap.o : treemap.cpp\r
- $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o\r
-\r
-\r
-# Item # 64 -- parsimonycommand --\r
-./parsimonycommand.o : parsimonycommand.cpp\r
- $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o\r
-\r
-\r
-# Item # 65 -- parsimony --\r
-./parsimony.o : parsimony.cpp\r
- $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o\r
-\r
-\r
-# Item # 66 -- seqsummarycommand --\r
-./seqsummarycommand.o : seqsummarycommand.cpp\r
- $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o\r
-\r
-\r
-# Item # 67 -- chimeraseqscommand --\r
-./chimeraseqscommand.o : chimeraseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o\r
-\r
-\r
-# Item # 68 -- sharedlistvector --\r
-./sharedlistvector.o : sharedlistvector.cpp\r
- $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o\r
-\r
-\r
-# Item # 69 -- tree --\r
-./tree.o : tree.cpp\r
- $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o\r
-\r
-\r
-# Item # 70 -- readtree --\r
-./readtree.o : readtree.cpp\r
- $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o\r
-\r
-\r
-# Item # 71 -- sharedsobscollectsummary --\r
-./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp\r
- $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o\r
-\r
-\r
-# Item # 72 -- deconvolutecommand --\r
-./deconvolutecommand.o : deconvolutecommand.cpp\r
- $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o\r
-\r
-\r
-# Item # 73 -- listseqscommand --\r
-./listseqscommand.o : listseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o\r
-\r
-\r
-# Item # 74 -- getseqscommand --\r
-./getseqscommand.o : getseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o\r
-\r
-\r
-# Item # 75 -- removeseqscommand --\r
-./removeseqscommand.o : removeseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o\r
-\r
-\r
-# Item # 76 -- systemcommand --\r
-./systemcommand.o : systemcommand.cpp\r
- $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o\r
-\r
-\r
-# Item # 77 -- binsequencecommand --\r
-./binsequencecommand.o : binsequencecommand.cpp\r
- $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o\r
-\r
-\r
-# Item # 78 -- distancecommand --\r
-./distancecommand.o : distancecommand.cpp\r
- $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o\r
-\r
-\r
-# Item # 79 -- ace --\r
-./ace.o : ace.cpp\r
- $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o\r
-\r
-\r
-# Item # 80 -- averagelinkage --\r
-./averagelinkage.o : averagelinkage.cpp\r
- $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o\r
-\r
-\r
-# Item # 81 -- bootstrap --\r
-./bootstrap.o : bootstrap.cpp\r
- $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o\r
-\r
-\r
-# Item # 82 -- calculator --\r
-./calculator.o : calculator.cpp\r
- $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o\r
-\r
-\r
-# Item # 83 -- chao1 --\r
-./chao1.o : chao1.cpp\r
- $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o\r
-\r
-\r
-# Item # 84 -- cluster --\r
-./cluster.o : cluster.cpp\r
- $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o\r
-\r
-\r
-# Item # 85 -- clustercommand --\r
-./clustercommand.o : clustercommand.cpp\r
- $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o\r
-\r
-\r
-# Item # 86 -- collect --\r
-./collect.o : collect.cpp\r
- $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o\r
-\r
-\r
-# Item # 87 -- collectcommand --\r
-./collectcommand.o : collectcommand.cpp\r
- $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o\r
-\r
-\r
-# Item # 88 -- collectsharedcommand --\r
-./collectsharedcommand.o : collectsharedcommand.cpp\r
- $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o\r
-\r
-\r
-# Item # 89 -- commandoptionparser --\r
-./commandoptionparser.o : commandoptionparser.cpp\r
- $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o\r
-\r
-\r
-# Item # 90 -- completelinkage --\r
-./completelinkage.o : completelinkage.cpp\r
- $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o\r
-\r
-\r
-# Item # 91 -- database --\r
-./database.o : database.cpp\r
- $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o\r
-\r
-\r
-# Item # 92 -- engine --\r
-./engine.o : engine.cpp\r
- $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o\r
-\r
-\r
-# Item # 93 -- fastamap --\r
-./fastamap.o : fastamap.cpp\r
- $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o\r
-\r
-\r
-# Item # 94 -- fileoutput --\r
-./fileoutput.o : fileoutput.cpp\r
- $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o\r
-\r
-\r
-# Item # 95 -- globaldata --\r
-./globaldata.o : globaldata.cpp\r
- $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o\r
-\r
-\r
-# Item # 96 -- groupmap --\r
-./groupmap.o : groupmap.cpp\r
- $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o\r
-\r
-\r
-# Item # 97 -- helpcommand --\r
-./helpcommand.o : helpcommand.cpp\r
- $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o\r
-\r
-\r
-# Item # 98 -- inputdata --\r
-./inputdata.o : inputdata.cpp\r
- $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o\r
-\r
-\r
-# Item # 99 -- jackknife --\r
-./jackknife.o : jackknife.cpp\r
- $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o\r
-\r
-\r
-# Item # 100 -- kmer --\r
-./kmer.o : kmer.cpp\r
- $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o\r
-\r
-\r
-# Item # 101 -- kmerdb --\r
-./kmerdb.o : kmerdb.cpp\r
- $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o\r
-\r
-\r
-# Item # 102 -- listvector --\r
-./listvector.o : listvector.cpp\r
- $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o\r
-\r
-\r
-# Item # 103 -- mothur --\r
-./mothur.o : mothur.cpp\r
- $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o\r
-\r
-\r
-# Item # 104 -- nameassignment --\r
-./nameassignment.o : nameassignment.cpp\r
- $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o\r
-\r
-\r
-# Item # 105 -- npshannon --\r
-./npshannon.o : npshannon.cpp\r
- $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o\r
-\r
-\r
-# Item # 106 -- ordervector --\r
-./ordervector.o : ordervector.cpp\r
- $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o\r
-\r
-\r
-# Item # 107 -- progress --\r
-./progress.o : progress.cpp\r
- $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o\r
-\r
-\r
-# Item # 108 -- quitcommand --\r
-./quitcommand.o : quitcommand.cpp\r
- $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o\r
-\r
-\r
-# Item # 109 -- rabundvector --\r
-./rabundvector.o : rabundvector.cpp\r
- $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o\r
-\r
-\r
-# Item # 110 -- rarecalc --\r
-./rarecalc.o : rarecalc.cpp\r
- $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o\r
-\r
-\r
-# Item # 111 -- raredisplay --\r
-./raredisplay.o : raredisplay.cpp\r
- $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o\r
-\r
-\r
-# Item # 112 -- rarefact --\r
-./rarefact.o : rarefact.cpp\r
- $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o\r
-\r
-\r
-# Item # 113 -- rarefactcommand --\r
-./rarefactcommand.o : rarefactcommand.cpp\r
- $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o\r
-\r
-\r
-# Item # 114 -- rarefactsharedcommand --\r
-./rarefactsharedcommand.o : rarefactsharedcommand.cpp\r
- $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o\r
-\r
-\r
-# Item # 115 -- sabundvector --\r
-./sabundvector.o : sabundvector.cpp\r
- $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o\r
-\r
-\r
-# Item # 116 -- sequence --\r
-./sequence.o : sequence.cpp\r
- $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o\r
-\r
-\r
-# Item # 117 -- shannon --\r
-./shannon.o : shannon.cpp\r
- $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o\r
-\r
-\r
-# Item # 118 -- sharedace --\r
-./sharedace.o : sharedace.cpp\r
- $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o\r
-\r
-\r
-# Item # 119 -- sharedchao1 --\r
-./sharedchao1.o : sharedchao1.cpp\r
- $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o\r
-\r
-\r
-# Item # 120 -- sharedcommand --\r
-./sharedcommand.o : sharedcommand.cpp\r
- $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o\r
-\r
-\r
-# Item # 121 -- sharedjabund --\r
-./sharedjabund.o : sharedjabund.cpp\r
- $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o\r
-\r
-\r
-# Item # 122 -- sharedjclass --\r
-./sharedjclass.o : sharedjclass.cpp\r
- $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o\r
-\r
-\r
-# Item # 123 -- sharedjest --\r
-./sharedjest.o : sharedjest.cpp\r
- $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o\r
-\r
-\r
-# Item # 124 -- sharedordervector --\r
-./sharedordervector.o : sharedordervector.cpp\r
- $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o\r
-\r
-\r
-# Item # 125 -- sharedrabundvector --\r
-./sharedrabundvector.o : sharedrabundvector.cpp\r
- $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o\r
-\r
-\r
-# Item # 126 -- sharedsabundvector --\r
-./sharedsabundvector.o : sharedsabundvector.cpp\r
- $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o\r
-\r
-\r
-# Item # 127 -- sharedsobs --\r
-./sharedsobs.o : sharedsobs.cpp\r
- $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o\r
-\r
-\r
-# Item # 128 -- sharedsorabund --\r
-./sharedsorabund.o : sharedsorabund.cpp\r
- $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o\r
-\r
-\r
-# Item # 129 -- sharedsorclass --\r
-./sharedsorclass.o : sharedsorclass.cpp\r
- $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o\r
-\r
-\r
-# Item # 130 -- sharedsorest --\r
-./sharedsorest.o : sharedsorest.cpp\r
- $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o\r
-\r
-\r
-# Item # 131 -- sharedthetan --\r
-./sharedthetan.o : sharedthetan.cpp\r
- $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o\r
-\r
-\r
-# Item # 132 -- sharedthetayc --\r
-./sharedthetayc.o : sharedthetayc.cpp\r
- $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o\r
-\r
-\r
-# Item # 133 -- simpson --\r
-./simpson.o : simpson.cpp\r
- $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o\r
-\r
-\r
-# Item # 134 -- singlelinkage --\r
-./singlelinkage.o : singlelinkage.cpp\r
- $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o\r
-\r
-\r
-# Item # 135 -- sparsematrix --\r
-./sparsematrix.o : sparsematrix.cpp\r
- $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o\r
-\r
-\r
-# Item # 136 -- summarycommand --\r
-./summarycommand.o : summarycommand.cpp\r
- $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o\r
-\r
-\r
-# Item # 137 -- summarysharedcommand --\r
-./summarysharedcommand.o : summarysharedcommand.cpp\r
- $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o\r
-\r
-\r
-# Item # 138 -- uvest --\r
-./uvest.o : uvest.cpp\r
- $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o\r
-\r
-\r
-# Item # 139 -- validcalculator --\r
-./validcalculator.o : validcalculator.cpp\r
- $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o\r
-\r
-\r
-# Item # 140 -- validparameter --\r
-./validparameter.o : validparameter.cpp\r
- $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o\r
-\r
-\r
-# Item # 141 -- treenode --\r
-./treenode.o : treenode.cpp\r
- $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o\r
-\r
-\r
-# Item # 142 -- readtreecommand --\r
-./readtreecommand.o : readtreecommand.cpp\r
- $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o\r
-\r
-\r
-# Item # 143 -- reversecommand --\r
-./reversecommand.o : reversecommand.cpp\r
- $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o\r
-\r
-\r
-# Item # 144 -- trimseqscommand --\r
-./trimseqscommand.o : trimseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o\r
-\r
-\r
-# Item # 145 -- slibshuff --\r
-./slibshuff.o : slibshuff.cpp\r
- $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o\r
-\r
-\r
-# Item # 146 -- libshuff --\r
-./libshuff.o : libshuff.cpp\r
- $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o\r
-\r
-\r
-# Item # 147 -- dlibshuff --\r
-./dlibshuff.o : dlibshuff.cpp\r
- $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o\r
-\r
-\r
-# Item # 148 -- mergefilecommand --\r
-./mergefilecommand.o : mergefilecommand.cpp\r
- $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o\r
-\r
-\r
-# Item # 149 -- coverage --\r
-./coverage.o : coverage.cpp\r
- $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o\r
-\r
-\r
-# Item # 150 -- whittaker --\r
-./whittaker.o : whittaker.cpp\r
- $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o\r
-\r
-\r
-# Item # 151 -- preclustercommand --\r
-./preclustercommand.o : preclustercommand.cpp\r
- $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o\r
-\r
-\r
-# Item # 152 -- otuhierarchycommand --\r
-./otuhierarchycommand.o : otuhierarchycommand.cpp\r
- $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o\r
-\r
-\r
-# Item # 153 -- setdircommand --\r
-./setdircommand.o : setdircommand.cpp\r
- $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o\r
-\r
-\r
-# Item # 154 -- getgroupcommand --\r
-./getgroupcommand.o : getgroupcommand.cpp\r
- $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o\r
-\r
-\r
-# Item # 155 -- getlabelcommand --\r
-./getlabelcommand.o : getlabelcommand.cpp\r
- $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o\r
-\r
-\r
-# Item # 156 -- secondarystructurecommand --\r
-./secondarystructurecommand.o : secondarystructurecommand.cpp\r
- $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o\r
-\r
-\r
-# Item # 157 -- mothurout --\r
-./mothurout.o : mothurout.cpp\r
- $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o\r
-\r
-\r
-# Item # 158 -- parselistscommand --\r
-./parselistscommand.o : parselistscommand.cpp\r
- $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o\r
-\r
-\r
-# Item # 159 -- readblast --\r
-./readblast.o : readblast.cpp\r
- $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o\r
-\r
-\r
-# Item # 160 -- chimeracheckrdp --\r
-./chimeracheckrdp.o : chimeracheckrdp.cpp\r
- $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o\r
-\r
-\r
-# Item # 161 -- hclustercommand --\r
-./hclustercommand.o : hclustercommand.cpp\r
- $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o\r
-\r
-\r
-# Item # 162 -- hcluster --\r
-./hcluster.o : hcluster.cpp\r
- $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o\r
-\r
-\r
-# Item # 163 -- getlistcountcommand --\r
-./getlistcountcommand.o : getlistcountcommand.cpp\r
- $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o\r
-\r
-\r
-# Item # 164 -- readcluster --\r
-./readcluster.o : readcluster.cpp\r
- $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o\r
-\r
-\r
-# Item # 165 -- ccode --\r
-./ccode.o : ccode.cpp\r
- $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o\r
-\r
-\r
-# Item # 166 -- taxonomyequalizer --\r
-./taxonomyequalizer.o : taxonomyequalizer.cpp\r
- $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o\r
-\r
-\r
-# Item # 167 -- phylotypecommand --\r
-./phylotypecommand.o : phylotypecommand.cpp\r
- $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o\r
-\r
-\r
-# Item # 168 -- classifyseqscommand --\r
-./classifyseqscommand.o : classifyseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o\r
-\r
-\r
-# Item # 169 -- classify --\r
-./classify.o : classify.cpp\r
- $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o\r
-\r
-\r
-# Item # 170 -- phylotree --\r
-./phylotree.o : phylotree.cpp\r
- $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o\r
-\r
-\r
-# Item # 171 -- bayesian --\r
-./bayesian.o : bayesian.cpp\r
- $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o\r
-\r
-\r
-# Item # 172 -- alignmentdb --\r
-./alignmentdb.o : alignmentdb.cpp\r
- $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o\r
-\r
-\r
-# Item # 173 -- knn --\r
-./knn.o : knn.cpp\r
- $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o\r
-\r
-\r
-# Item # 174 -- distancedb --\r
-./distancedb.o : distancedb.cpp\r
- $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o\r
-\r
-\r
-# Item # 175 -- chimeraslayer --\r
-./chimeraslayer.o : chimeraslayer.cpp\r
- $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o\r
-\r
-\r
-# Item # 176 -- slayer --\r
-./slayer.o : slayer.cpp\r
- $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o\r
-\r
-\r
-# Item # 177 -- pcacommand --\r
-./pcacommand.o : pcacommand.cpp\r
- $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o\r
-\r
-\r
-# Item # 178 -- formatcolumn --\r
-./formatcolumn.o : formatcolumn.cpp\r
- $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o\r
-\r
-\r
-# Item # 179 -- formatphylip --\r
-./formatphylip.o : formatphylip.cpp\r
- $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o\r
-\r
-\r
-# Item # 180 -- mgclustercommand --\r
-./mgclustercommand.o : mgclustercommand.cpp\r
- $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o\r
-\r
-\r
-# Item # 181 -- getsharedotucommand --\r
-./getsharedotucommand.o : getsharedotucommand.cpp\r
- $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o\r
-\r
-\r
-# Item # 182 -- maligner --\r
-./maligner.o : maligner.cpp\r
- $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o\r
-\r
-\r
-# Item # 183 -- chimerarealigner --\r
-./chimerarealigner.o : chimerarealigner.cpp\r
- $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o\r
-\r
-\r
-# Item # 184 -- bergerparker --\r
-./bergerparker.o : bergerparker.cpp\r
- $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o\r
-\r
-\r
-# Item # 185 -- bstick --\r
-./bstick.o : bstick.cpp\r
- $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o\r
-\r
-\r
-# Item # 186 -- sharedkstest --\r
-./sharedkstest.o : sharedkstest.cpp\r
- $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o\r
-\r
-\r
-# Item # 187 -- qstat --\r
-./qstat.o : qstat.cpp\r
- $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o\r
-\r
-\r
-# Item # 188 -- shen --\r
-./shen.o : shen.cpp\r
- $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o\r
-\r
-\r
-# Item # 189 -- logsd --\r
-./logsd.o : logsd.cpp\r
- $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o\r
-\r
-\r
-# Item # 190 -- geom --\r
-./geom.o : geom.cpp\r
- $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o\r
-\r
-# Item # 191 -- parsesffcommand --\r
-./parsesffcommand.o : parsesffcommand.cpp\r
- $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o\r
-\r
-# Item # 192 -- chimeraccodecommand --\r
-./chimeraccodecommand.o : chimeraccodecommand.cpp\r
- $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o\r
-\r
-# Item # 193 -- chimeracheckcommand --\r
-./chimeracheckcommand.o : chimeracheckcommand.cpp\r
- $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o\r
-\r
-\r
-# Item # 194 -- chimeraslayercommand --\r
-./chimeraslayercommand.o : chimeraslayercommand.cpp\r
- $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o\r
-\r
-# Item # 195 -- chimerapintailcommand --\r
-./chimerapintailcommand.o : chimerapintailcommand.cpp\r
- $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o\r
-\r
-# Item # 196 -- chimerabellerophoncommand --\r
-./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp\r
- $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o\r
-\r
-# Item # 197 -- phylosummary --\r
-./phylosummary.o : phylosummary.cpp\r
- $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o\r
-\r
-# Item # 198 -- setlogfilecommand --\r
-./setlogfilecommand.o : setlogfilecommand.cpp\r
- $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o\r
-\r
-# Item # 199 -- phylodiversity --\r
-./phylodiversity.o : phylodiversity.cpp\r
- $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o\r
-\r
-# Item # 200 -- phylodiversitycommand --\r
-./phylodiversitycommand.o : phylodiversitycommand.cpp\r
- $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o\r
-\r
-# Item # 201 -- makegroupcommand --\r
-./makegroupcommand.o : makegroupcommand.cpp\r
- $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o\r
-\r
-# Item # 202 -- chopseqscommand --\r
-./chopseqscommand.o : chopseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o\r
-\r
-# Item # 203 -- clearcutcommand --\r
-./clearcutcommand.o : clearcutcommand.cpp\r
- $(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o\r
-\r
-# Item # 204 -- catchallcommand --\r
-./catchallcommand.o : catchallcommand.cpp\r
- $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o\r
-\r
-# Item # 205 -- splitabundcommand --\r
-./splitabundcommand.o : splitabundcommand.cpp\r
- $(CC) $(CC_OPTIONS) splitabundcommand.cpp -c $(INCLUDE) -o ./splitabundcommand.o\r
- \r
-# Item # 206 -- splitmatrix --\r
-./splitmatrix.o : splitmatrix.cpp\r
- $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o\r
- \r
-# Item # 207 -- clustersplit --\r
-./clustersplitcommand.o : clustersplitcommand.cpp\r
- $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o\r
- \r
-# Item # 208 -- classifyotu --\r
-./classifyotucommand.o : classifyotucommand.cpp\r
- $(CC) $(CC_OPTIONS) classifyotucommand.cpp -c $(INCLUDE) -o ./classifyotucommand.o\r
-\r
-# Item # 209 -- splitmatrix --\r
-./weightedlinkage.o : weightedlinkage.cpp\r
- $(CC) $(CC_OPTIONS) weightedlinkage.cpp -c $(INCLUDE) -o ./weightedlinkage.o\r
-\r
-##### END RUN ####\r
+###################################################
+#
+# Makefile for mothur
+# Created: June 29, 2010
+#
+###################################################
+
+#
+# Macros
+#
+
+USEMPI ?= no
+64BIT_VERSION ?= yes
+USEREADLINE ?= yes
+CYGWIN_BUILD ?= no
+USECOMPRESSION ?= no
+MOTHUR_FILES="\"Enter_your_default_path_here\""
+RELEASE_DATE = "\"10/16/2013\""
+VERSION = "\"1.32.1\""
+FORTAN_COMPILER = gfortran
+FORTRAN_FLAGS =
+
+# Optimize to level 3:
+CXXFLAGS += -O3
+
+ifeq ($(strip $(64BIT_VERSION)),yes)
+ #if you are using centos uncomment the following lines
+ #CXX = g++44
+
+ #if you are a mac user use the following line
+ TARGET_ARCH += -arch x86_64
+
+ #if you using cygwin to build Windows the following line
+ #CXX = x86_64-w64-mingw32-g++
+ #CC = x86_64-w64-mingw32-g++
+ #FORTAN_COMPILER = x86_64-w64-mingw32-gfortran
+ #TARGET_ARCH += -m64 -static
+
+ #if you are a linux user use the following line
+ #CXXFLAGS += -mtune=native -march=native
+
+ CXXFLAGS += -DBIT_VERSION
+endif
+
+
+CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
+
+ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
+else
+ CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
+endif
+
+ifeq ($(strip $(CYGWIN_BUILD)),yes)
+ CXXFLAGS += -mno-cygwin
+ LDFLAGS += -mno-cygwin
+endif
+
+# if you do not want to use the readline library, set this to no.
+# make sure you have the library installed
+
+
+ifeq ($(strip $(USEREADLINE)),yes)
+ CXXFLAGS += -DUSE_READLINE
+ LIBS = \
+ -lreadline\
+ -lncurses
+endif
+
+
+ifeq ($(strip $(USEMPI)),yes)
+ CXX = mpic++
+ CXXFLAGS += -DUSE_MPI
+endif
+
+# if you want to enable reading and writing of compressed files, set to yes.
+# The default is no. this may only work on unix-like systems, not for windows.
+
+
+ifeq ($(strip $(USECOMPRESSION)),yes)
+ CXXFLAGS += -DUSE_COMPRESSION
+endif
+
+#
+# INCLUDE directories for mothur
+#
+
+ CXXFLAGS += -I.
+
+#
+# Get the list of all .cpp files, rename to .o files
+#
+
+OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
+OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f))
+
+mothur : fortranSource $(OBJECTS) uchime
+ $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
+
+ strip mothur
+
+uchime:
+ cd uchime_src && ./mk && mv uchime .. && cd ..
+
+fortranSource:
+ ${FORTAN_COMPILER} -c $(FORTRAN_FLAGS) *.f
+
+install : mothur
+# cp mothur ../Release/mothur
+
+%.o : %.c %.h
+ $(COMPILE.c) $(OUTPUT_OPTION) $<
+%.o : %.cpp %.h
+ $(COMPILE.cpp) $(OUTPUT_OPTION) $<
+%.o : %.cpp %.hpp
+ $(COMPILE.cpp) $(OUTPUT_OPTION) $<
+
+
+clean :
+ @rm -f $(OBJECTS)
+ @rm -f uchime
+
projects / mothur.git / blobdiff