enabled ~

[mothur.git] / makefile

diff --git a/makefile b/makefile
index d4aac7f8f4fc2252cb51ab17ca553f36b265de00..a868ec524c0366e2e942c4a57379b4248a619569 100644 (file)
--- a/makefile
+++ b/makefile
@@ -26,7 +26,8 @@ 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_OPTIONS += -DUSE_MPI\r
@@ -218,7 +219,9 @@ mothur : \
                ./classifyseqscommand.o\\r
                ./parsesffcommand.o\\r
                ./classify.o\\r
-               ./phylotree.o\\r
+               ./phylotree.o\
+               ./phylodiversity.o\
+               ./phylodiversitycommand.o\\r
                ./bayesian.o\
                ./phylosummary.o\\r
                ./alignmentdb.o\\r
@@ -239,7 +242,8 @@ mothur : \
                ./qstat.o\\r
                ./shen.o\\r
                ./logsd.o\\r
-               ./geom.o\r
+               ./geom.o\
+               ./setlogfilecommand.o\r
        $(CC) $(LNK_OPTIONS) \\r
                ./sharedutilities.o\\r
                ./treegroupscommand.o\\r
@@ -416,7 +420,9 @@ mothur : \
                ./classifyseqscommand.o\\r
                ./parsesffcommand.o\\r
                ./classify.o\\r
-               ./phylotree.o\\r
+               ./phylotree.o\
+               ./phylodiversity.o\
+               ./phylodiversitycommand.o\\r
                ./bayesian.o\
                ./phylosummary.o\\r
                ./alignmentdb.o\\r
@@ -437,7 +443,8 @@ mothur : \
                ./qstat.o\\r
                ./shen.o\\r
                ./logsd.o\\r
-               ./geom.o\\r
+               ./geom.o\
+               ./setlogfilecommand.o\\r
                -o ../Release/mothur\r
 \r
 clean : \r
@@ -617,7 +624,9 @@ clean :
                ./classifyseqscommand.o\\r
                ./parsesffcommand.o\\r
                ./classify.o\\r
-               ./phylotree.o\\r
+               ./phylotree.o\
+               ./phylodiversity.o\
+               ./phylodiversitycommand.o\\r
                ./bayesian.o\
                ./phylosummary.o\\r
                ./alignmentdb.o\\r
@@ -638,7 +647,8 @@ clean :
                ./qstat.o\\r
                ./shen.o\\r
                ./logsd.o\\r
-               ./geom.o\\r
+               ./geom.o\
+               ./setlogfilecommand.o\\r
                mothur\r
 \r
 install : mothur\r
@@ -1623,9 +1633,21 @@ install : mothur
 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp\r
        $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o\r
 
-# Item # 171 -- phylosummary --\r
+# Item # 197 -- phylosummary --\r
 ./phylosummary.o : phylosummary.cpp\r
        $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o\r
+
+# Item # 198 -- setlogfilecommand --\r
+./setlogfilecommand.o : setlogfilecommand.cpp\r
+       $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o\r
+\r
+# Item # 199 -- phylodiversity --\r
+./phylodiversity.o : phylodiversity.cpp\r
+       $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o\r
+\r
+# Item # 200 -- phylodiversitycommand --\r
+./phylodiversitycommand.o : phylodiversitycommand.cpp\r
+       $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o\r
 \r
 \r
 \r