# Macros\r
#\r
\r
-CC = g++\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
-L../readline-6.0\r
endif\r
\r
-USEMPI ?= no
-\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
-
- INCLUDE = -I.
+\r
+ INCLUDE = -I.\r
\r
#\r
# Build mothur\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
./taxonomyequalizer.o\\r
./phylotypecommand.o\\r
./classifyseqscommand.o\\r
+ ./classifyotucommand.o\\r
./parsesffcommand.o\\r
./classify.o\\r
- ./phylotree.o\
- ./phylodiversity.o\
+ ./phylotree.o\\r
+ ./phylodiversity.o\\r
./phylodiversitycommand.o\\r
- ./bayesian.o\
+ ./bayesian.o\\r
./phylosummary.o\\r
./alignmentdb.o\\r
./knn.o\\r
./qstat.o\\r
./shen.o\\r
./logsd.o\\r
- ./geom.o\
+ ./geom.o\\r
./setlogfilecommand.o\r
$(CC) $(LNK_OPTIONS) \\r
./sharedutilities.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
./taxonomyequalizer.o\\r
./phylotypecommand.o\\r
./classifyseqscommand.o\\r
+ ./classifyotucommand.o\\r
./parsesffcommand.o\\r
./classify.o\\r
- ./phylotree.o\
- ./phylodiversity.o\
+ ./phylotree.o\\r
+ ./phylodiversity.o\\r
./phylodiversitycommand.o\\r
- ./bayesian.o\
+ ./bayesian.o\\r
./phylosummary.o\\r
./alignmentdb.o\\r
./knn.o\\r
./qstat.o\\r
./shen.o\\r
./logsd.o\\r
- ./geom.o\
+ ./geom.o\\r
./setlogfilecommand.o\\r
-o mothur\r
\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
./taxonomyequalizer.o\\r
./phylotypecommand.o\\r
./classifyseqscommand.o\\r
+ ./classifyotucommand.o\\r
./parsesffcommand.o\\r
./classify.o\\r
- ./phylotree.o\
- ./phylodiversity.o\
+ ./phylotree.o\\r
+ ./phylodiversity.o\\r
./phylodiversitycommand.o\\r
- ./bayesian.o\
+ ./bayesian.o\\r
./phylosummary.o\\r
./alignmentdb.o\\r
./knn.o\\r
./qstat.o\\r
./shen.o\\r
./logsd.o\\r
- ./geom.o\
+ ./geom.o\\r
./setlogfilecommand.o\\r
mothur\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
./phylodiversitycommand.o : phylodiversitycommand.cpp\r
$(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o\r
\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 -- weightedlinkage --\r
+./weightedlinkage.o : weightedlinkage.cpp\r
+ $(CC) $(CC_OPTIONS) weightedlinkage.cpp -c $(INCLUDE) -o ./weightedlinkage.o\r
\r
##### END RUN ####\r