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|
Makefile | 8 +++---
scripts/Makefile | 6 +++-
scripts/aln2wig/Makefile | 8 +++---
scripts/compileSpliceCands/Makefile | 6 ++--
src/Makefile | 43 ++++++++++++++++++----------------
5 files changed, 38 insertions(+), 33 deletions(-)
diff --git a/Makefile b/Makefile
index e23a667..64610c8 100644
--- a/Makefile
+++ b/Makefile
@@ -3,9 +3,9 @@
#
all:
- cd src && ${MAKE}
- cd scripts && ${MAKE}
+ $(MAKE) -C src
+ $(MAKE) -C scripts
clean:
- cd src && ${MAKE} clean
- cd scripts && ${MAKE} clean
+ $(MAKE) -C src clean
+ $(MAKE) -C scripts clean
diff --git a/scripts/Makefile b/scripts/Makefile
index 6d4dd67..ab6a885 100644
--- a/scripts/Makefile
+++ b/scripts/Makefile
@@ -1,5 +1,7 @@
all :
- cd aln2wig && ${MAKE}
+ $(MAKE) -C aln2wig
+ $(MAKE) -C compileSpliceCands
clean :
- cd aln2wig && ${MAKE} clean
+ $(MAKE) -C aln2wig clean
+ $(MAKE) -C compileSpliceCands
diff --git a/scripts/aln2wig/Makefile b/scripts/aln2wig/Makefile
index 64d09f5..9752980 100644
--- a/scripts/aln2wig/Makefile
+++ b/scripts/aln2wig/Makefile
@@ -1,10 +1,10 @@
-CFLAGS := -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic -O2 -ggdb
+CFLAGS += -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic
psl2wig : aln2wig.o
- gcc $(CFLAGS) -o aln2wig aln2wig.o;
- cp aln2wig ../../bin
+ $(CC) $(CFLAGS) $(LDFLAGS) -o aln2wig aln2wig.o;
+ cp aln2wig ../../bin/
psl2wig.o : aln2wig.c
- gcc $(CFLAGS) -c aln2wig.c
+ $(CC) $(CFLAGS) -c aln2wig.c
all : psl2wig
diff --git a/scripts/compileSpliceCands/Makefile b/scripts/compileSpliceCands/Makefile
index cddada5..8079791 100644
--- a/scripts/compileSpliceCands/Makefile
+++ b/scripts/compileSpliceCands/Makefile
@@ -1,8 +1,8 @@
compileSpliceCands : compileSpliceCands.o list.h list.o
- gcc -o compileSpliceCands compileSpliceCands.o list.o;
-# cp compileSpliceCands ../../bin
+ $(CC) $(CFLAGS) $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o;
+ cp compileSpliceCands ../../bin/
compileSpliceCands.o : compileSpliceCands.c
- gcc -Wall -pedantic -ansi -c compileSpliceCands.c
+ $(CC) $(CFLAGS) -Wall -pedantic -ansi -c compileSpliceCands.c
all : compileSpliceCands
diff --git a/src/Makefile b/src/Makefile
index 71795b6..732b953 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -6,8 +6,8 @@
# a strict signed-only usage strategy to avoid mistakes since we are not warned about this.
# - In the current version, the order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh)
#
-CC = g++
-CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O2 ${CFLAGS} -static # -pg -DDEBUG -g -ggdb -static
+CXX ?= g++
+CXXFLAGS += -Wall -Wno-sign-compare -ansi -pedantic # -pg -DDEBUG -g -ggdb -static
INCLS = -I../include -I.
LIBS = # -lcwd
OBJS = genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o \
@@ -18,45 +18,48 @@ TOBJS = commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o # conte
PROGR = augustus etraining consensusFinder curve2hints fastBlockSearch prepareAlign
INFO = cflags
-all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info
+all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info bin
.SUFFIXES:
.SUFFIXES: .cc .o .so
.cc.o:
- $(CC) -c $(CFLAGS) -o $@ $< $(INCLS)
+ $(CXX) -c $(CXXFLAGS) -o $@ $< $(INCLS)
-augustus: augustus.cc $(OBJS) $(DUMOBJS)
- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+bin: $(PROGR)
+ cp $(PROGR) ../bin/
+
+augustus: augustus.o $(OBJS) $(DUMOBJS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
cp augustus ../bin/
-etraining: etraining.cc $(TOBJS) $(OBJS)
- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+etraining: etraining.o $(TOBJS) $(OBJS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
cp etraining ../bin/
-evaluate: evaluate.cc $(OBJS) $(DUMOBJS)
- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+evaluate: evaluate.o $(OBJS) $(DUMOBJS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
-consensusFinder: consensusFinder.cc consensus.o
- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+consensusFinder: consensusFinder.o consensus.o
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
-curve2hints: curve2hints.cc exon_seg.o
- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+curve2hints: curve2hints.o exon_seg.o
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
-fastBlockSearch: fastBlockSearch.cc pp_fastBlockSearcher.o \
+fastBlockSearch: fastBlockSearch.o pp_fastBlockSearcher.o \
types.o properties.o geneticcode.o pp_profile.o lldouble.o
- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
cp fastBlockSearch ../bin/
-prepareAlign: pp_prepare_align.cc
- $(CC) $(CFLAGS) -o $@ $^
+prepareAlign: pp_prepare_align.o
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^
cp prepareAlign ../bin/
info:
- echo "$(CFLAGS)" > $(INFO)
+ echo "$(CXXFLAGS)" > $(INFO)
clean:
- rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO)
+ rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ../bin/*
tidy: clean
rm -f *~ *.o *.rej *.orig ../include/*~ ../include/*.orig ../include/*.rej $(INFO)
|
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