reworked the classifiers summary file added groupfile option to classify.seqs, added...

[mothur.git] / makefile

diff --git a/makefile b/makefile
index 99152863384e31256a81f9e946862c588b2e6c58..d4aac7f8f4fc2252cb51ab17ca553f36b265de00 100644 (file)
--- a/makefile
+++ b/makefile
@@ -12,7 +12,6 @@
 \r
 CC = mpic++\r
 CC_OPTIONS = -O3\r
-LNK_OPTIONS = \r
 \r
 # if you do not want to use the readline library set to no, default yes.\r
 # make sure you have the library installed\r
@@ -27,7 +26,7 @@ ifeq  ($(strip $(USEREADLINE)),yes)
       -L../readline-6.0\r
 endif\r
 \r
-USEMPI ?= yes\r
+USEMPI ?= no\r
 \r
 ifeq  ($(strip $(USEMPI)),yes)\r
     CC_OPTIONS += -DUSE_MPI\r
@@ -220,7 +219,8 @@ mothur : \
                ./parsesffcommand.o\\r
                ./classify.o\\r
                ./phylotree.o\\r
-               ./bayesian.o\\r
+               ./bayesian.o\
+               ./phylosummary.o\\r
                ./alignmentdb.o\\r
                ./knn.o\\r
                ./distancedb.o\\r
@@ -417,7 +417,8 @@ mothur : \
                ./parsesffcommand.o\\r
                ./classify.o\\r
                ./phylotree.o\\r
-               ./bayesian.o\\r
+               ./bayesian.o\
+               ./phylosummary.o\\r
                ./alignmentdb.o\\r
                ./knn.o\\r
                ./distancedb.o\\r
@@ -617,7 +618,8 @@ clean :
                ./parsesffcommand.o\\r
                ./classify.o\\r
                ./phylotree.o\\r
-               ./bayesian.o\\r
+               ./bayesian.o\
+               ./phylosummary.o\\r
                ./alignmentdb.o\\r
                ./knn.o\\r
                ./distancedb.o\\r
@@ -1620,6 +1622,11 @@ install : mothur
 # Item # 196 -- chimerabellerophoncommand --\r
 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp\r
        $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o\r
+
+# Item # 171 -- phylosummary --\r
+./phylosummary.o : phylosummary.cpp\r
+       $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o\r
+\r
 \r
 \r
 ##### END RUN ####\r