X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=ef5cfe7ebb9550c5b5fa275e128f1ff013585e33;hb=8ef6687c1f586285d01c000cc5e359bf9c07c717;hp=5812d4551f9c6cc635f8ed4ee5bde2505a4b18df;hpb=6f4b9401f7deb8aaf0d87659298308f4138cc3b0;p=mothur.git

diff --git a/makefile b/makefile
index 5812d45..ef5cfe7 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.
@@ -29,14 +29,15 @@ endif
 USEMPI ?= no
 
 ifeq  ($(strip $(USEMPI)),yes)
+	CC = mpic++
     CC_OPTIONS += -DUSE_MPI
 endif
 
 #
 # INCLUDE directories for mothur
 #
-
-     INCLUDE = -I.
+
+     INCLUDE = -I.
 
 #
 # Build mothur
@@ -145,6 +146,14 @@ mothur : \
 		./globaldata.o\
 		./groupmap.o\
 		./helpcommand.o\
+		./makegroupcommand.o\
+		./chopseqscommand.o\
+		./clearcutcommand.o\
+		./catchallcommand.o\
+		./splitabundcommand.o\
+		./splitmatrix.o\
+		./clustersplitcommand.o\
+		./weightedlinkage.o\
 		./inputdata.o\
 		./jackknife.o\
 		./kmer.o\
@@ -216,11 +225,14 @@ mothur : \
 		./taxonomyequalizer.o\
 		./phylotypecommand.o\
 		./classifyseqscommand.o\
+		./classifyotucommand.o\
 		./parsesffcommand.o\
 		./classify.o\
 		./phylotree.o\
-		./bayesian.o\
-		./rawtrainingdatamaker.o\
+		./phylodiversity.o\
+		./phylodiversitycommand.o\
+		./bayesian.o\
+		./phylosummary.o\
 		./alignmentdb.o\
 		./knn.o\
 		./distancedb.o\
@@ -239,7 +251,8 @@ mothur : \
 		./qstat.o\
 		./shen.o\
 		./logsd.o\
-		./geom.o
+		./geom.o\
+		./setlogfilecommand.o
 	$(CC) $(LNK_OPTIONS) \
 		./sharedutilities.o\
 		./treegroupscommand.o\
@@ -343,6 +356,14 @@ mothur : \
 		./globaldata.o\
 		./groupmap.o\
 		./helpcommand.o\
+		./makegroupcommand.o\
+		./chopseqscommand.o\
+		./clearcutcommand.o\
+		./catchallcommand.o\
+		./splitabundcommand.o\
+		./splitmatrix.o\
+		./clustersplitcommand.o\
+		./weightedlinkage.o\
 		./inputdata.o\
 		./jackknife.o\
 		./kmer.o\
@@ -414,11 +435,14 @@ mothur : \
 		./taxonomyequalizer.o\
 		./phylotypecommand.o\
 		./classifyseqscommand.o\
+		./classifyotucommand.o\
 		./parsesffcommand.o\
 		./classify.o\
 		./phylotree.o\
-		./bayesian.o\
-		./rawtrainingdatamaker.o\
+		./phylodiversity.o\
+		./phylodiversitycommand.o\
+		./bayesian.o\
+		./phylosummary.o\
 		./alignmentdb.o\
 		./knn.o\
 		./distancedb.o\
@@ -438,7 +462,8 @@ mothur : \
 		./shen.o\
 		./logsd.o\
 		./geom.o\
-		-o ../Release/mothur
+		./setlogfilecommand.o\
+		-o mothur
 
 clean : 
 		rm \
@@ -544,6 +569,14 @@ clean :
 		./globaldata.o\
 		./groupmap.o\
 		./helpcommand.o\
+		./makegroupcommand.o\
+		./chopseqscommand.o\
+		./clearcutcommand.o\
+		./catchallcommand.o\
+		./splitabundcommand.o\
+		./splitmatrix.o\
+		./clustersplitcommand.o\
+		./weightedlinkage.o\
 		./inputdata.o\
 		./jackknife.o\
 		./kmer.o\
@@ -615,11 +648,14 @@ clean :
 		./taxonomyequalizer.o\
 		./phylotypecommand.o\
 		./classifyseqscommand.o\
+		./classifyotucommand.o\
 		./parsesffcommand.o\
 		./classify.o\
 		./phylotree.o\
-		./bayesian.o\
-		./rawtrainingdatamaker.o\
+		./phylodiversity.o\
+		./phylodiversitycommand.o\
+		./bayesian.o\
+		./phylosummary.o\
 		./alignmentdb.o\
 		./knn.o\
 		./distancedb.o\
@@ -639,6 +675,7 @@ clean :
 		./shen.o\
 		./logsd.o\
 		./geom.o\
+		./setlogfilecommand.o\
 		mothur
 
 install : mothur
@@ -1622,11 +1659,57 @@ install : mothur
 # Item # 196 -- chimerabellerophoncommand --
 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp
 	$(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o
-
-# Item # 171 -- rawtrainingdatamaker --
-./rawtrainingdatamaker.o : rawtrainingdatamaker.cpp
-	$(CC) $(CC_OPTIONS) rawtrainingdatamaker.cpp -c $(INCLUDE) -o ./rawtrainingdatamaker.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.cpp
+	$(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o
+	
+# Item # 207 -- clustersplit --
+./clustersplitcommand.o : clustersplitcommand.cpp
+	$(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o
+	
+# Item # 208 -- classifyotu --
+./classifyotucommand.o : classifyotucommand.cpp
+	$(CC) $(CC_OPTIONS) classifyotucommand.cpp -c $(INCLUDE) -o ./classifyotucommand.o
+
+# Item # 209 -- weightedlinkage --
+./weightedlinkage.o : weightedlinkage.cpp
+	$(CC) $(CC_OPTIONS) weightedlinkage.cpp -c $(INCLUDE) -o ./weightedlinkage.o
 
 ##### END RUN ####