153 lines
4.1 KiB
Diff
153 lines
4.1 KiB
Diff
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)
|