added make.group command

[mothur.git] / makefile

diff --git a/makefile b/makefile
index d95b5ef31c04f2e119136d2cc0d146bb2343397b..ea9f9ac8a62e05e350b93cc5ce7a26f628f6a895 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
@@ -144,7 +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
@@ -218,8 +220,11 @@ mothur : \
                ./classifyseqscommand.o\\r
                ./parsesffcommand.o\\r
                ./classify.o\\r
-               ./phylotree.o\\r
-               ./bayesian.o\\r
+               ./phylotree.o\
+               ./phylodiversity.o\
+               ./phylodiversitycommand.o\\r
+               ./bayesian.o\
+               ./phylosummary.o\\r
                ./alignmentdb.o\\r
                ./knn.o\\r
                ./distancedb.o\\r
@@ -238,7 +243,8 @@ 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
@@ -341,7 +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
@@ -415,8 +422,11 @@ mothur : \
                ./classifyseqscommand.o\\r
                ./parsesffcommand.o\\r
                ./classify.o\\r
-               ./phylotree.o\\r
-               ./bayesian.o\\r
+               ./phylotree.o\
+               ./phylodiversity.o\
+               ./phylodiversitycommand.o\\r
+               ./bayesian.o\
+               ./phylosummary.o\\r
                ./alignmentdb.o\\r
                ./knn.o\\r
                ./distancedb.o\\r
@@ -435,7 +445,8 @@ 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
@@ -541,7 +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
@@ -615,8 +627,11 @@ clean :
                ./classifyseqscommand.o\\r
                ./parsesffcommand.o\\r
                ./classify.o\\r
-               ./phylotree.o\\r
-               ./bayesian.o\\r
+               ./phylotree.o\
+               ./phylodiversity.o\
+               ./phylodiversitycommand.o\\r
+               ./bayesian.o\
+               ./phylosummary.o\\r
                ./alignmentdb.o\\r
                ./knn.o\\r
                ./distancedb.o\\r
@@ -635,7 +650,8 @@ clean :
                ./qstat.o\\r
                ./shen.o\\r
                ./logsd.o\\r
-               ./geom.o\\r
+               ./geom.o\
+               ./setlogfilecommand.o\\r
                mothur\r
 \r
 install : mothur\r
@@ -1619,6 +1635,26 @@ install : mothur
 # Item # 196 -- chimerabellerophoncommand --\r
 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp\r
        $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o\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
+# 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