added make.group command

[mothur.git] / makefile

diff --git a/makefile b/makefile
index b15c44bbc235be6b21f7c4c2b7822c7aac0772d2..ea9f9ac8a62e05e350b93cc5ce7a26f628f6a895 100644 (file)
--- a/makefile
+++ b/makefile
@@ -10,7 +10,7 @@
 # Macros\r
 #\r
 \r
-CC = mpic++\r
+CC = g++\r
 CC_OPTIONS = -O3\r
 \r
 # if you do not want to use the readline library set to no, default yes.\r
@@ -26,7 +26,7 @@ ifeq  ($(strip $(USEREADLINE)),yes)
       -L../readline-6.0\r
 endif\r
 \r
-USEMPI ?= yes
+USEMPI ?= no
 \r
 \r
 ifeq  ($(strip $(USEMPI)),yes)\r
@@ -145,7 +145,8 @@ mothur : \
                ./fileoutput.o\\r
                ./globaldata.o\\r
                ./groupmap.o\\r
-               ./helpcommand.o\\r
+               ./helpcommand.o\
+               ./makegroupcommand.o\\r
                ./inputdata.o\\r
                ./jackknife.o\\r
                ./kmer.o\\r
@@ -219,7 +220,9 @@ 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
@@ -344,7 +347,8 @@ mothur : \
                ./fileoutput.o\\r
                ./globaldata.o\\r
                ./groupmap.o\\r
-               ./helpcommand.o\\r
+               ./helpcommand.o\
+               ./makegroupcommand.o\\r
                ./inputdata.o\\r
                ./jackknife.o\\r
                ./kmer.o\\r
@@ -418,7 +422,9 @@ 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
@@ -546,7 +552,8 @@ clean :
                ./fileoutput.o\\r
                ./globaldata.o\\r
                ./groupmap.o\\r
-               ./helpcommand.o\\r
+               ./helpcommand.o\
+               ./makegroupcommand.o\\r
                ./inputdata.o\\r
                ./jackknife.o\\r
                ./kmer.o\\r
@@ -620,7 +627,9 @@ 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
@@ -1635,6 +1644,17 @@ install : mothur
 ./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
+# Item # 201 -- makegroupcommand --\r
+./makegroupcommand.o : makegroupcommand.cpp\r
+       $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o\r
 \r
 \r
 ##### END RUN ####\r