| sources/makefile | 15 +++++-------- |
| train/makefile | 59 +++++++++++++++++++++++++++++++---------------------- |
| 2 files changed, 40 insertions(+), 34 deletions(-) |
| |
| 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 2383f18..d5a7107 100644 |
| --- a/train/makefile |
| +++ b/train/makefile |
| @@ -2,9 +2,6 @@ |
| |
| # C compiler |
| |
| -C = gcc |
| -CC = g++ |
| -CFLAGS = -O1 ${SEARCHDIRS} |
| #CFLAGS = -O3 -g -Wall |
| LIBS = -lm |
| |
| @@ -15,64 +12,76 @@ 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) -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) -o $@ build-icm-noframe.o misc.o $(LIBS) |
| + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm-noframe.o misc.o $(LIBS) |
| |
| build1: build1.o |
| - ${CC} build1.c -o build1 $(LIBS) |
| + $(CXX) $(CXXFLAGS) $(LDFLAGS) build1.c -o build1 $(LIBS) |
| |
| build2: build2.o |
| - ${CC} build2.c -o build2 $(LIBS) |
| + $(CXX) $(CXXFLAGS) $(LDFLAGS) build2.c -o build2 $(LIBS) |
| |
| falsecomp: falsecomp.o |
| - ${CC} falsecomp.c -o falsecomp $(LIBS) |
| + $(CXX) $(CXXFLAGS) $(LDFLAGS) falsecomp.c -o falsecomp $(LIBS) |
| |
| findsites: findsites.o |
| - ${CC} findsites.c -o findsites $(LIBS) |
| + $(CXX) $(CXXFLAGS) $(LDFLAGS) findsites.c -o findsites $(LIBS) |
| |
| karlin: karlin.o |
| - ${CC} karlin.c -o karlin $(LIBS) |
| + $(CXX) $(CXXFLAGS) $(LDFLAGS) karlin.c -o karlin $(LIBS) |
| |
| score: score.o |
| - ${CC} score.c -o score $(LIBS) |
| + $(CXX) $(CXXFLAGS) $(LDFLAGS) score.c -o score $(LIBS) |
| |
| score2: score2.o |
| - ${CC} score2.c -o score2 $(LIBS) |
| + $(CXX) $(CXXFLAGS) $(LDFLAGS) score2.c -o score2 $(LIBS) |
| |
| scoreATG: scoreATG.o |
| - ${CC} scoreATG.c -o scoreATG $(LIBS) |
| + $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG.c -o scoreATG $(LIBS) |
| |
| scoreATG2: scoreATG2.o |
| - ${CC} scoreATG2.c -o scoreATG2 $(LIBS) |
| + $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG2.c -o scoreATG2 $(LIBS) |
| |
| scoreSTOP: scoreSTOP.o |
| - ${CC} scoreSTOP.c -o scoreSTOP $(LIBS) |
| + $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP.c -o scoreSTOP $(LIBS) |
| |
| escoreSTOP2: scoreSTOP2.o |
| - ${CC} scoreSTOP2.c -o scoreSTOP2 $(LIBS) |
| + $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP2.c -o scoreSTOP2 $(LIBS) |
| |
| -rfapp: erfapp.o |
| - ${CC} erfapp.c -o erfapp $(LIBS) |
| +erfapp: erfapp.o |
| + $(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) |