X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=0c5adac54141a6864ab5cf2a1565f58e92aeab38;hb=7837a9bfdfccdc26360987a44c389832fdb82651;hp=a868ec524c0366e2e942c4a57379b4248a619569;hpb=dabb32850eae34e26b066a7da55716ad685786a3;p=mothur.git

diff --git a/makefile b/makefile
index a868ec5..0c5adac 100644
--- a/makefile
+++ b/makefile
@@ -10,7 +10,7 @@
 # Macros
 #
 
-CC = mpic++
+CC = g++ 
 CC_OPTIONS = -O3
 
 # if you do not want to use the readline library set to no, default yes.
@@ -26,18 +26,18 @@ ifeq  ($(strip $(USEREADLINE)),yes)
       -L../readline-6.0
 endif
 
-USEMPI ?= no
-
+USEMPI ?= yes
 
 ifeq  ($(strip $(USEMPI)),yes)
+	CC = mpic++
     CC_OPTIONS += -DUSE_MPI
 endif
 
 #
 # INCLUDE directories for mothur
 #
-
-     INCLUDE = -I.
+
+     INCLUDE = -I.
 
 #
 # Build mothur
@@ -146,6 +146,13 @@ mothur : \
 		./globaldata.o\
 		./groupmap.o\
 		./helpcommand.o\
+		./makegroupcommand.o\
+		./chopseqscommand.o\
+		./clearcutcommand.o\
+		./catchallcommand.o\
+		./splitabundcommand.o\
+		./splitmatrix.o\
+		./clustersplitcommand.o\
 		./inputdata.o\
 		./jackknife.o\
 		./kmer.o\
@@ -219,10 +226,10 @@ mothur : \
 		./classifyseqscommand.o\
 		./parsesffcommand.o\
 		./classify.o\
-		./phylotree.o\
-		./phylodiversity.o\
+		./phylotree.o\
+		./phylodiversity.o\
 		./phylodiversitycommand.o\
-		./bayesian.o\
+		./bayesian.o\
 		./phylosummary.o\
 		./alignmentdb.o\
 		./knn.o\
@@ -242,7 +249,7 @@ mothur : \
 		./qstat.o\
 		./shen.o\
 		./logsd.o\
-		./geom.o\
+		./geom.o\
 		./setlogfilecommand.o
 	$(CC) $(LNK_OPTIONS) \
 		./sharedutilities.o\
@@ -347,6 +354,13 @@ mothur : \
 		./globaldata.o\
 		./groupmap.o\
 		./helpcommand.o\
+		./makegroupcommand.o\
+		./chopseqscommand.o\
+		./clearcutcommand.o\
+		./catchallcommand.o\
+		./splitabundcommand.o\
+		./splitmatrix.o\
+		./clustersplitcommand.o\
 		./inputdata.o\
 		./jackknife.o\
 		./kmer.o\
@@ -420,10 +434,10 @@ mothur : \
 		./classifyseqscommand.o\
 		./parsesffcommand.o\
 		./classify.o\
-		./phylotree.o\
-		./phylodiversity.o\
+		./phylotree.o\
+		./phylodiversity.o\
 		./phylodiversitycommand.o\
-		./bayesian.o\
+		./bayesian.o\
 		./phylosummary.o\
 		./alignmentdb.o\
 		./knn.o\
@@ -443,7 +457,7 @@ mothur : \
 		./qstat.o\
 		./shen.o\
 		./logsd.o\
-		./geom.o\
+		./geom.o\
 		./setlogfilecommand.o\
 		-o ../Release/mothur
 
@@ -551,6 +565,13 @@ clean :
 		./globaldata.o\
 		./groupmap.o\
 		./helpcommand.o\
+		./makegroupcommand.o\
+		./chopseqscommand.o\
+		./clearcutcommand.o\
+		./catchallcommand.o\
+		./splitabundcommand.o\
+		./splitmatrix.o\
+		./clustersplitcommand.o\
 		./inputdata.o\
 		./jackknife.o\
 		./kmer.o\
@@ -624,10 +645,10 @@ clean :
 		./classifyseqscommand.o\
 		./parsesffcommand.o\
 		./classify.o\
-		./phylotree.o\
-		./phylodiversity.o\
+		./phylotree.o\
+		./phylodiversity.o\
 		./phylodiversitycommand.o\
-		./bayesian.o\
+		./bayesian.o\
 		./phylosummary.o\
 		./alignmentdb.o\
 		./knn.o\
@@ -647,7 +668,7 @@ clean :
 		./qstat.o\
 		./shen.o\
 		./logsd.o\
-		./geom.o\
+		./geom.o\
 		./setlogfilecommand.o\
 		mothur
 
@@ -1632,11 +1653,11 @@ install : mothur
 # Item # 196 -- chimerabellerophoncommand --
 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp
 	$(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o
-
+
 # Item # 197 -- phylosummary --
 ./phylosummary.o : phylosummary.cpp
 	$(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o
-
+
 # Item # 198 -- setlogfilecommand --
 ./setlogfilecommand.o : setlogfilecommand.cpp
 	$(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o
@@ -1649,6 +1670,32 @@ install : mothur
 ./phylodiversitycommand.o : phylodiversitycommand.cpp
 	$(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o
 
-
+# Item # 201 -- makegroupcommand --
+./makegroupcommand.o : makegroupcommand.cpp
+	$(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o
+
+# Item # 202 -- chopseqscommand --
+./chopseqscommand.o : chopseqscommand.cpp
+	$(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o
+
+# Item # 203 -- clearcutcommand --
+./clearcutcommand.o : clearcutcommand.cpp
+	$(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o
+
+# Item # 204 -- catchallcommand --
+./catchallcommand.o : catchallcommand.cpp
+	$(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o
+
+# Item # 205 -- splitabundcommand --
+./splitabundcommand.o : splitabundcommand.cpp
+	$(CC) $(CC_OPTIONS) splitabundcommand.cpp -c $(INCLUDE) -o ./splitabundcommand.o
+	
+# Item # 206 -- splitmatrix --
+./splitmatrix.o : splitmatrix.cpp
+	$(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o
+	
+# Item # 207 -- splitmatrix --
+./clustersplitcommand.o : clustersplitcommand.cpp
+	$(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o
 
 ##### END RUN ####