X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=fdcef2794c06cb81c399376aaf79518246c23aca;hb=62568a297aaf939ab753334f17abde82ec8e8531;hp=99152863384e31256a81f9e946862c588b2e6c58;hpb=438aa88dbc092d9c1c80ec3fa20c8e47f97101c4;p=mothur.git

diff --git a/makefile b/makefile
index 9915286..fdcef27 100644
--- a/makefile
+++ b/makefile
@@ -10,9 +10,8 @@
 # Macros
 #
 
-CC = mpic++
+CC = g++ 
 CC_OPTIONS = -O3
-LNK_OPTIONS = 
 
 # if you do not want to use the readline library set to no, default yes.
 # make sure you have the library installed
@@ -27,17 +26,18 @@ ifeq  ($(strip $(USEREADLINE)),yes)
       -L../readline-6.0
 endif
 
-USEMPI ?= yes
+USEMPI ?= no
 
 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\
@@ -220,7 +227,10 @@ mothur : \
 		./parsesffcommand.o\
 		./classify.o\
 		./phylotree.o\
+		./phylodiversity.o\
+		./phylodiversitycommand.o\
 		./bayesian.o\
+		./phylosummary.o\
 		./alignmentdb.o\
 		./knn.o\
 		./distancedb.o\
@@ -239,7 +249,8 @@ mothur : \
 		./qstat.o\
 		./shen.o\
 		./logsd.o\
-		./geom.o
+		./geom.o\
+		./setlogfilecommand.o
 	$(CC) $(LNK_OPTIONS) \
 		./sharedutilities.o\
 		./treegroupscommand.o\
@@ -343,6 +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\
@@ -417,7 +435,10 @@ mothur : \
 		./parsesffcommand.o\
 		./classify.o\
 		./phylotree.o\
+		./phylodiversity.o\
+		./phylodiversitycommand.o\
 		./bayesian.o\
+		./phylosummary.o\
 		./alignmentdb.o\
 		./knn.o\
 		./distancedb.o\
@@ -437,6 +458,7 @@ mothur : \
 		./shen.o\
 		./logsd.o\
 		./geom.o\
+		./setlogfilecommand.o\
 		-o ../Release/mothur
 
 clean : 
@@ -543,6 +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\
@@ -617,7 +646,10 @@ clean :
 		./parsesffcommand.o\
 		./classify.o\
 		./phylotree.o\
+		./phylodiversity.o\
+		./phylodiversitycommand.o\
 		./bayesian.o\
+		./phylosummary.o\
 		./alignmentdb.o\
 		./knn.o\
 		./distancedb.o\
@@ -637,6 +669,7 @@ clean :
 		./shen.o\
 		./logsd.o\
 		./geom.o\
+		./setlogfilecommand.o\
 		mothur
 
 install : mothur
@@ -1621,5 +1654,48 @@ install : mothur
 ./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
+
+# Item # 199 -- phylodiversity --
+./phylodiversity.o : phylodiversity.cpp
+	$(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o
+
+# Item # 200 -- phylodiversitycommand --
+./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.o
+	$(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 ####