added classify.otu command

[mothur.git] / makefile

diff --git a/makefile b/makefile
index b421ca2db2f17149198ecb0edc9839903fdccf31..a9732412c6168e2c5c9e2a8f0dabdd1a1fdcdbc9 100644 (file)
--- a/makefile
+++ b/makefile
@@ -10,7 +10,7 @@
 # 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
@@ -26,18 +26,18 @@ ifeq  ($(strip $(USEREADLINE)),yes)
       -L../readline-6.0\r
 endif\r
 \r
-USEMPI ?= no
-\r
+USEMPI ?= no\r
 \r
 ifeq  ($(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
@@ -146,6 +146,13 @@ mothur : \
                ./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
                ./inputdata.o\\r
                ./jackknife.o\\r
                ./kmer.o\\r
@@ -217,12 +224,13 @@ mothur : \
                ./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
@@ -242,7 +250,7 @@ mothur : \
                ./qstat.o\\r
                ./shen.o\\r
                ./logsd.o\\r
-               ./geom.o\
+               ./geom.o\\r
                ./setlogfilecommand.o\r
        $(CC) $(LNK_OPTIONS) \\r
                ./sharedutilities.o\\r
@@ -347,6 +355,13 @@ mothur : \
                ./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
                ./inputdata.o\\r
                ./jackknife.o\\r
                ./kmer.o\\r
@@ -418,12 +433,13 @@ mothur : \
                ./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
@@ -443,9 +459,9 @@ mothur : \
                ./qstat.o\\r
                ./shen.o\\r
                ./logsd.o\\r
-               ./geom.o\
+               ./geom.o\\r
                ./setlogfilecommand.o\\r
-               -o mothur\r
+               -o ../Release/mothur\r
 \r
 clean : \r
                rm \\r
@@ -551,6 +567,13 @@ clean :
                ./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
                ./inputdata.o\\r
                ./jackknife.o\\r
                ./kmer.o\\r
@@ -622,12 +645,13 @@ clean :
                ./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
@@ -647,7 +671,7 @@ clean :
                ./qstat.o\\r
                ./shen.o\\r
                ./logsd.o\\r
-               ./geom.o\
+               ./geom.o\\r
                ./setlogfilecommand.o\\r
                mothur\r
 \r
@@ -1632,11 +1656,11 @@ install : mothur
 # 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
@@ -1649,6 +1673,37 @@ install : mothur
 ./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 -- splitmatrix --\r
+./clustersplitcommand.o : clustersplitcommand.cpp\r
+       $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o\r
+       \r
+# Item # 207 -- splitmatrix --\r
+./classifyotucommand.o : classifyotucommand.cpp\r
+       $(CC) $(CC_OPTIONS) classifyotucommand.cpp -c $(INCLUDE) -o ./classifyotucommand.o\r
 \r
 \r
 ##### END RUN ####\r