added mpi code to cluster.split command

[mothur.git] / makefile

diff --git a/makefile b/makefile
index f4af8e9b02a92cc0c9bf1d282ec5cacf9d0514f8..08dee23581723953d2001a36ccda1cc957538eef 100644 (file)
--- a/makefile
+++ b/makefile
@@ -10,12 +10,19 @@
 # Macros
 #
 
-CC = g++
-CC_OPTIONS = -O3
+CC = g++ 
+CC_OPTIONS = -O3 
 
 # if you do not want to use the readline library set to no, default yes.
 # make sure you have the library installed
 
+64BIT_VERSION ?= yes
+
+ifeq  ($(strip $(64BIT_VERSION)),yes)
+    CC_OPTIONS += -arch x86_64
+       LNK_OPTIONS += -arch x86_64
+endif
+
 USEREADLINE ?= yes
 
 ifeq  ($(strip $(USEREADLINE)),yes)
@@ -26,7 +33,7 @@ ifeq  ($(strip $(USEREADLINE)),yes)
       -L../readline-6.0
 endif
 
-USEMPI ?= yes
+USEMPI ?= no
 
 ifeq  ($(strip $(USEMPI)),yes)
        CC = mpic++
@@ -124,6 +131,7 @@ mothur : \
                ./listseqscommand.o\
                ./getseqscommand.o\
                ./removeseqscommand.o\
+               ./degapseqscommand.o\
                ./systemcommand.o\
                ./binsequencecommand.o\
                ./distancecommand.o\
@@ -153,6 +161,7 @@ mothur : \
                ./splitabundcommand.o\
                ./splitmatrix.o\
                ./clustersplitcommand.o\
+               ./weightedlinkage.o\
                ./inputdata.o\
                ./jackknife.o\
                ./kmer.o\
@@ -219,11 +228,13 @@ mothur : \
                ./hclustercommand.o\
                ./hcluster.o\
                ./getlistcountcommand.o\
+               ./getrelabundcommand.o\
                ./readcluster.o\
                ./ccode.o\
                ./taxonomyequalizer.o\
                ./phylotypecommand.o\
                ./classifyseqscommand.o\
+               ./classifyotucommand.o\
                ./parsesffcommand.o\
                ./classify.o\
                ./phylotree.o\
@@ -332,6 +343,7 @@ mothur : \
                ./listseqscommand.o\
                ./getseqscommand.o\
                ./removeseqscommand.o\
+               ./degapseqscommand.o\
                ./systemcommand.o\
                ./binsequencecommand.o\
                ./distancecommand.o\
@@ -361,6 +373,7 @@ mothur : \
                ./splitabundcommand.o\
                ./splitmatrix.o\
                ./clustersplitcommand.o\
+               ./weightedlinkage.o\
                ./inputdata.o\
                ./jackknife.o\
                ./kmer.o\
@@ -427,11 +440,13 @@ mothur : \
                ./hclustercommand.o\
                ./hcluster.o\
                ./getlistcountcommand.o\
+               ./getrelabundcommand.o\
                ./readcluster.o\
                ./ccode.o\
                ./taxonomyequalizer.o\
                ./phylotypecommand.o\
                ./classifyseqscommand.o\
+               ./classifyotucommand.o\
                ./parsesffcommand.o\
                ./classify.o\
                ./phylotree.o\
@@ -543,6 +558,7 @@ clean :
                ./listseqscommand.o\
                ./getseqscommand.o\
                ./removeseqscommand.o\
+               ./degapseqscommand.o\
                ./systemcommand.o\
                ./binsequencecommand.o\
                ./distancecommand.o\
@@ -572,6 +588,7 @@ clean :
                ./splitabundcommand.o\
                ./splitmatrix.o\
                ./clustersplitcommand.o\
+               ./weightedlinkage.o\
                ./inputdata.o\
                ./jackknife.o\
                ./kmer.o\
@@ -638,11 +655,13 @@ clean :
                ./hclustercommand.o\
                ./hcluster.o\
                ./getlistcountcommand.o\
+               ./getrelabundcommand.o\
                ./readcluster.o\
                ./ccode.o\
                ./taxonomyequalizer.o\
                ./phylotypecommand.o\
                ./classifyseqscommand.o\
+               ./classifyotucommand.o\
                ./parsesffcommand.o\
                ./classify.o\
                ./phylotree.o\
@@ -1687,15 +1706,31 @@ install : mothur
        $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o
 
 # Item # 205 -- splitabundcommand --
-./splitabundcommand : splitabundcommand
-       $(CC) $(CC_OPTIONS) splitabundcommand -c $(INCLUDE) -o ./splitabundcommand
+./splitabundcommand.o : splitabundcommand.cpp
+       $(CC) $(CC_OPTIONS) splitabundcommand.cpp -c $(INCLUDE) -o ./splitabundcommand.o
        
 # Item # 206 -- splitmatrix --
-./splitmatrix : splitmatrix
-       $(CC) $(CC_OPTIONS) splitmatrix -c $(INCLUDE) -o ./splitmatrix
+./splitmatrix.o : splitmatrix.cpp
+       $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o
+       
+# Item # 207 -- clustersplit --
+./clustersplitcommand.o : clustersplitcommand.cpp
+       $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o
        
-# Item # 207 -- splitmatrix --
-./clustersplitcommand : clustersplitcommand
-       $(CC) $(CC_OPTIONS) clustersplitcommand -c $(INCLUDE) -o ./clustersplitcommand
+# Item # 208 -- classifyotu --
+./classifyotucommand.o : classifyotucommand.cpp
+       $(CC) $(CC_OPTIONS) classifyotucommand.cpp -c $(INCLUDE) -o ./classifyotucommand.o
+
+# Item # 209 -- weightedlinkage --
+./weightedlinkage.o : weightedlinkage.cpp
+       $(CC) $(CC_OPTIONS) weightedlinkage.cpp -c $(INCLUDE) -o ./weightedlinkage.o
+       
+# Item # 210 -- degapseqscommand --
+./degapseqscommand.o : degapseqscommand.cpp
+       $(CC) $(CC_OPTIONS) degapseqscommand.cpp -c $(INCLUDE) -o ./degapseqscommand.o
+
+# Item # 211 -- getrelabundcommand --
+./getrelabundcommand.o : getrelabundcommand.cpp
+       $(CC) $(CC_OPTIONS) getrelabundcommand.cpp -c $(INCLUDE) -o ./getrelabundcommand.o
 
 ##### END RUN ####