changes to chop.seqs

[mothur.git] / makefile

diff --git a/makefile b/makefile
index 451d613a24d3e91dd025f6f584f63f9ec5a2404a..fdcef2794c06cb81c399376aaf79518246c23aca 100644 (file)
--- a/makefile
+++ b/makefile
@@ -2,7 +2,7 @@
 #\r
 # Makefile for mothur\r
 # Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]\r
-# Created: [Thu Mar  4 08:31:03 2010]\r
+# Created: April 16, 2010\r
 #\r
 ###################################################\r
 \r
@@ -10,9 +10,8 @@
 # Macros\r
 #\r
 \r
-CC = mpic++\r
+CC = g++ \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
@@ -30,14 +29,15 @@ endif
 USEMPI ?= no\r
 \r
 ifeq  ($(strip $(USEMPI)),yes)\r
+       CC = mpic++\r
     CC_OPTIONS += -DUSE_MPI\r
 endif\r
 \r
 #\r
 # INCLUDE directories for mothur\r
 #\r
-
-     INCLUDE = -I.
+\r
+     INCLUDE = -I.\r
 \r
 #\r
 # Build mothur\r
@@ -146,6 +146,13 @@ mothur : \
                ./globaldata.o\\r
                ./groupmap.o\\r
                ./helpcommand.o\\r
+               ./makegroupcommand.o\\r
+               ./chopseqscommand.o\\r
+               ./clearcutcommand.o\\r
+               ./catchallcommand.o\\r
+               ./splitabundcommand.o\\r
+               ./splitmatrix.o\\r
+               ./clustersplitcommand.o\\r
                ./inputdata.o\\r
                ./jackknife.o\\r
                ./kmer.o\\r
@@ -220,7 +227,10 @@ mothur : \
                ./parsesffcommand.o\\r
                ./classify.o\\r
                ./phylotree.o\\r
+               ./phylodiversity.o\\r
+               ./phylodiversitycommand.o\\r
                ./bayesian.o\\r
+               ./phylosummary.o\\r
                ./alignmentdb.o\\r
                ./knn.o\\r
                ./distancedb.o\\r
@@ -239,7 +249,8 @@ mothur : \
                ./qstat.o\\r
                ./shen.o\\r
                ./logsd.o\\r
-               ./geom.o\r
+               ./geom.o\\r
+               ./setlogfilecommand.o\r
        $(CC) $(LNK_OPTIONS) \\r
                ./sharedutilities.o\\r
                ./treegroupscommand.o\\r
@@ -343,6 +354,13 @@ mothur : \
                ./globaldata.o\\r
                ./groupmap.o\\r
                ./helpcommand.o\\r
+               ./makegroupcommand.o\\r
+               ./chopseqscommand.o\\r
+               ./clearcutcommand.o\\r
+               ./catchallcommand.o\\r
+               ./splitabundcommand.o\\r
+               ./splitmatrix.o\\r
+               ./clustersplitcommand.o\\r
                ./inputdata.o\\r
                ./jackknife.o\\r
                ./kmer.o\\r
@@ -417,7 +435,10 @@ mothur : \
                ./parsesffcommand.o\\r
                ./classify.o\\r
                ./phylotree.o\\r
+               ./phylodiversity.o\\r
+               ./phylodiversitycommand.o\\r
                ./bayesian.o\\r
+               ./phylosummary.o\\r
                ./alignmentdb.o\\r
                ./knn.o\\r
                ./distancedb.o\\r
@@ -437,6 +458,7 @@ mothur : \
                ./shen.o\\r
                ./logsd.o\\r
                ./geom.o\\r
+               ./setlogfilecommand.o\\r
                -o ../Release/mothur\r
 \r
 clean : \r
@@ -543,6 +565,13 @@ clean :
                ./globaldata.o\\r
                ./groupmap.o\\r
                ./helpcommand.o\\r
+               ./makegroupcommand.o\\r
+               ./chopseqscommand.o\\r
+               ./clearcutcommand.o\\r
+               ./catchallcommand.o\\r
+               ./splitabundcommand.o\\r
+               ./splitmatrix.o\\r
+               ./clustersplitcommand.o\\r
                ./inputdata.o\\r
                ./jackknife.o\\r
                ./kmer.o\\r
@@ -617,7 +646,10 @@ clean :
                ./parsesffcommand.o\\r
                ./classify.o\\r
                ./phylotree.o\\r
+               ./phylodiversity.o\\r
+               ./phylodiversitycommand.o\\r
                ./bayesian.o\\r
+               ./phylosummary.o\\r
                ./alignmentdb.o\\r
                ./knn.o\\r
                ./distancedb.o\\r
@@ -637,6 +669,7 @@ clean :
                ./shen.o\\r
                ./logsd.o\\r
                ./geom.o\\r
+               ./setlogfilecommand.o\\r
                mothur\r
 \r
 install : mothur\r
@@ -1621,5 +1654,48 @@ install : mothur
 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp\r
        $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o\r
 \r
+# Item # 197 -- phylosummary --\r
+./phylosummary.o : phylosummary.cpp\r
+       $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o\r
+\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
+# Item # 202 -- chopseqscommand --\r
+./chopseqscommand.o : chopseqscommand.cpp\r
+       $(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o\r
+\r
+# Item # 203 -- clearcutcommand --\r
+./clearcutcommand.o : clearcutcommand.cpp\r
+       $(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o\r
+\r
+# Item # 204 -- catchallcommand --\r
+./catchallcommand.o : catchallcommand.cpp\r
+       $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o\r
+\r
+# Item # 205 -- splitabundcommand --\r
+./splitabundcommand.o : splitabundcommand.cpp\r
+       $(CC) $(CC_OPTIONS) splitabundcommand.cpp -c $(INCLUDE) -o ./splitabundcommand.o\r
+       \r
+# Item # 206 -- splitmatrix --\r
+./splitmatrix.o : splitmatrix.o\r
+       $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o\r
+       \r
+# Item # 207 -- splitmatrix --\r
+./clustersplitcommand.o : clustersplitcommand.cpp\r
+       $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o\r
 \r
 ##### END RUN ####\r