pat's mod to trim.seqs

[mothur.git] / makefile

diff --git a/makefile b/makefile
index 0c5adac54141a6864ab5cf2a1565f58e92aeab38..ef5cfe7ebb9550c5b5fa275e128f1ff013585e33 100644 (file)
--- a/makefile
+++ b/makefile
@@ -26,7 +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 = mpic++\r
@@ -153,6 +153,7 @@ mothur : \
                ./splitabundcommand.o\\r
                ./splitmatrix.o\\r
                ./clustersplitcommand.o\\r
+               ./weightedlinkage.o\\r
                ./inputdata.o\\r
                ./jackknife.o\\r
                ./kmer.o\\r
@@ -224,6 +225,7 @@ mothur : \
                ./taxonomyequalizer.o\\r
                ./phylotypecommand.o\\r
                ./classifyseqscommand.o\\r
+               ./classifyotucommand.o\\r
                ./parsesffcommand.o\\r
                ./classify.o\\r
                ./phylotree.o\\r
@@ -361,6 +363,7 @@ mothur : \
                ./splitabundcommand.o\\r
                ./splitmatrix.o\\r
                ./clustersplitcommand.o\\r
+               ./weightedlinkage.o\\r
                ./inputdata.o\\r
                ./jackknife.o\\r
                ./kmer.o\\r
@@ -432,6 +435,7 @@ mothur : \
                ./taxonomyequalizer.o\\r
                ./phylotypecommand.o\\r
                ./classifyseqscommand.o\\r
+               ./classifyotucommand.o\\r
                ./parsesffcommand.o\\r
                ./classify.o\\r
                ./phylotree.o\\r
@@ -459,7 +463,7 @@ mothur : \
                ./logsd.o\\r
                ./geom.o\\r
                ./setlogfilecommand.o\\r
-               -o ../Release/mothur\r
+               -o mothur\r
 \r
 clean : \r
                rm \\r
@@ -572,6 +576,7 @@ clean :
                ./splitabundcommand.o\\r
                ./splitmatrix.o\\r
                ./clustersplitcommand.o\\r
+               ./weightedlinkage.o\\r
                ./inputdata.o\\r
                ./jackknife.o\\r
                ./kmer.o\\r
@@ -643,6 +648,7 @@ clean :
                ./taxonomyequalizer.o\\r
                ./phylotypecommand.o\\r
                ./classifyseqscommand.o\\r
+               ./classifyotucommand.o\\r
                ./parsesffcommand.o\\r
                ./classify.o\\r
                ./phylotree.o\\r
@@ -1694,8 +1700,16 @@ install : mothur
 ./splitmatrix.o : splitmatrix.cpp\r
        $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o\r
        \r
-# Item # 207 -- splitmatrix --\r
+# Item # 207 -- clustersplit --\r
 ./clustersplitcommand.o : clustersplitcommand.cpp\r
        $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o\r
+       \r
+# Item # 208 -- classifyotu --\r
+./classifyotucommand.o : classifyotucommand.cpp\r
+       $(CC) $(CC_OPTIONS) classifyotucommand.cpp -c $(INCLUDE) -o ./classifyotucommand.o\r
+\r
+# Item # 209 -- weightedlinkage --\r
+./weightedlinkage.o : weightedlinkage.cpp\r
+       $(CC) $(CC_OPTIONS) weightedlinkage.cpp -c $(INCLUDE) -o ./weightedlinkage.o\r
 \r
 ##### END RUN ####\r