X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=b421ca2db2f17149198ecb0edc9839903fdccf31;hb=8130a55348ef2b5f431fe47c6a83aae581e244b5;hp=d95b5ef31c04f2e119136d2cc0d146bb2343397b;hpb=813f0516e9c7533859f57ebe6d7b8854896bf009;p=mothur.git

diff --git a/makefile b/makefile
index d95b5ef..b421ca2 100644
--- a/makefile
+++ b/makefile
@@ -26,7 +26,8 @@ ifeq  ($(strip $(USEREADLINE)),yes)
       -L../readline-6.0
 endif
 
-USEMPI ?= no
+USEMPI ?= no
+
 
 ifeq  ($(strip $(USEMPI)),yes)
     CC_OPTIONS += -DUSE_MPI
@@ -218,8 +219,11 @@ mothur : \
 		./classifyseqscommand.o\
 		./parsesffcommand.o\
 		./classify.o\
-		./phylotree.o\
-		./bayesian.o\
+		./phylotree.o\
+		./phylodiversity.o\
+		./phylodiversitycommand.o\
+		./bayesian.o\
+		./phylosummary.o\
 		./alignmentdb.o\
 		./knn.o\
 		./distancedb.o\
@@ -238,7 +242,8 @@ mothur : \
 		./qstat.o\
 		./shen.o\
 		./logsd.o\
-		./geom.o
+		./geom.o\
+		./setlogfilecommand.o
 	$(CC) $(LNK_OPTIONS) \
 		./sharedutilities.o\
 		./treegroupscommand.o\
@@ -415,8 +420,11 @@ mothur : \
 		./classifyseqscommand.o\
 		./parsesffcommand.o\
 		./classify.o\
-		./phylotree.o\
-		./bayesian.o\
+		./phylotree.o\
+		./phylodiversity.o\
+		./phylodiversitycommand.o\
+		./bayesian.o\
+		./phylosummary.o\
 		./alignmentdb.o\
 		./knn.o\
 		./distancedb.o\
@@ -435,8 +443,9 @@ mothur : \
 		./qstat.o\
 		./shen.o\
 		./logsd.o\
-		./geom.o\
-		-o ../Release/mothur
+		./geom.o\
+		./setlogfilecommand.o\
+		-o mothur
 
 clean : 
 		rm \
@@ -615,8 +624,11 @@ clean :
 		./classifyseqscommand.o\
 		./parsesffcommand.o\
 		./classify.o\
-		./phylotree.o\
-		./bayesian.o\
+		./phylotree.o\
+		./phylodiversity.o\
+		./phylodiversitycommand.o\
+		./bayesian.o\
+		./phylosummary.o\
 		./alignmentdb.o\
 		./knn.o\
 		./distancedb.o\
@@ -635,7 +647,8 @@ clean :
 		./qstat.o\
 		./shen.o\
 		./logsd.o\
-		./geom.o\
+		./geom.o\
+		./setlogfilecommand.o\
 		mothur
 
 install : mothur
@@ -1619,6 +1632,23 @@ 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
+
+# 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
+
 
 
 ##### END RUN ####