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diff --git a/sources/makefile b/sources/makefile
index f287d71..c560f48 100644
--- a/sources/makefile
+++ b/sources/makefile
@@ -2,25 +2,22 @@
-CC=g++
-CFLAGS=-g
-
all: glimmerhmm
glimmerhmm: glimmerhmm.o graph.o sites.o tree_util_prob.o util.o
- $(CC) $(CFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o -lm
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o -lm
glimmerhmm.o: glimmerhmm.c
- $(CC) $(CFLAGS) -c glimmerhmm.c
+ $(CXX) $(CXXFLAGS) -c glimmerhmm.c
graph.o: graph.c
- $(CC) $(CFLAGS) -c graph.c
+ $(CXX) $(CXXFLAGS) -c graph.c
sites.o: sites.c
- $(CC) $(CFLAGS) -c sites.c
+ $(CXX) $(CXXFLAGS) -c sites.c
tree_util_prob.o: tree_util_prob.c
- $(CC) $(CFLAGS) -c tree_util_prob.c
+ $(CXX) $(CXXFLAGS) -c tree_util_prob.c
util.o: util.c
- $(CC) $(CFLAGS) -c util.c
+ $(CXX) $(CXXFLAGS) -c util.c
diff --git a/train/makefile b/train/makefile
index 56eaa13..d660cf1 100644
--- a/train/makefile
+++ b/train/makefile
@@ -2,11 +2,8 @@
# C compiler
-C = gcc
-CC = g++
#CFLAGS = -O1 ${SEARCHDIRS}
#CFLAGS = -O3 -g -Wall
-CFLAGS = -Wall -g
LIBS = -lm
MAKEFILE= makefile
@@ -16,67 +13,79 @@ all: build-icm build-icm-noframe build1 build2 falsecomp findsites karlin sco
misc.o: misc.c
- ${C} ${CFLAGS} -c misc.c
+ $(CC) $(CFLAGS) -c misc.c
build-icm.o: build-icm.c
- ${C} ${CFLAGS} -c build-icm.c
+ $(CC) $(CFLAGS) -c build-icm.c
build-icm: build-icm.o misc.o
- $(C) ${CFLAGS} -o $@ build-icm.o misc.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm.o misc.o $(LIBS)
build-icm-noframe.o: build-icm-noframe.c
- ${C} ${CFLAGS} -c build-icm-noframe.c
+ $(CC) $(CFLAGS) -c build-icm-noframe.c
build-icm-noframe: build-icm-noframe.o misc.o
- $(C) ${CFLAGS} -o $@ build-icm-noframe.o misc.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm-noframe.o misc.o $(LIBS)
build1: build1.o
- ${CC} ${CFLAGS} build1.c -o build1 $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) build1.o -o build1 $(LIBS)
build2: build2.o
- ${CC} ${CFLAGS} build2.c -o build2 $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) build2.o -o build2 $(LIBS)
falsecomp: falsecomp.o
- ${CC} ${CFLAGS} falsecomp.c -o falsecomp $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) falsecomp.o -o falsecomp $(LIBS)
findsites: findsites.o
- ${CC} ${CFLAGS} findsites.c -o findsites $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) findsites.o -o findsites $(LIBS)
karlin: karlin.o
- ${CC} ${CFLAGS} karlin.c -o karlin $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) karlin.o -o karlin $(LIBS)
score: score.o
- ${CC} ${CFLAGS} score.c -o score $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) score.o -o score $(LIBS)
score2: score2.o
- ${CC} ${CFLAGS} score2.c -o score2 $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) score2.o -o score2 $(LIBS)
scoreATG: scoreATG.o
- ${CC} ${CFLAGS} scoreATG.c -o scoreATG $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG.o -o scoreATG $(LIBS)
scoreATG2: scoreATG2.o
- ${CC} ${CFLAGS} scoreATG2.c -o scoreATG2 $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG2.o -o scoreATG2 $(LIBS)
scoreSTOP: scoreSTOP.o
- ${CC} ${CFLAGS} scoreSTOP.c -o scoreSTOP $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP.o -o scoreSTOP $(LIBS)
escoreSTOP2: scoreSTOP2.o
- ${CC} ${CFLAGS} scoreSTOP2.c -o scoreSTOP2 $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP2.o -o scoreSTOP2 $(LIBS)
rfapp: erfapp.o
- ${CC} ${CFLAGS} erfapp.c -o erfapp $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) erfapp.c -o erfapp $(LIBS)
sites.o: sites.c
- ${CC} ${CFLAGS} -c sites.c
+ $(CXX) $(CXXFLAGS) -c sites.c
+
+scoreATG.o: scoreATG.c
+ $(CXX) $(CXXFLAGS) -c scoreATG.c
+
+scoreSTOP.o: scoreSTOP.c
+ $(CXX) $(CXXFLAGS) -c scoreSTOP.c
+
+scoreSTOP2.o: scoreSTOP2.c
+ $(CXX) $(CXXFLAGS) -c scoreSTOP2.c
+
+scoreATG2.o: scoreATG2.c
+ $(CXX) $(CXXFLAGS) -c scoreATG2.c
utils.o: utils.c
- ${CC} ${CFLAGS} -c utils.c
+ $(CXX) $(CXXFLAGS) -c utils.c
splicescore.o: splicescore.c
- ${CC} ${CFLAGS} -c splicescore.c
+ $(CXX) $(CXXFLAGS) -c splicescore.c
splicescore: splicescore.o sites.o utils.o
- ${CC} splicescore.o sites.o utils.o -o splicescore $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) splicescore.o sites.o utils.o -o splicescore $(LIBS)
.PHONY : clean
clean::
/bin/rm -f core* splicescore *.o score build? build-icm \
|
