You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
149 lines
5.3 KiB
149 lines
5.3 KiB
src/Makefile | 61 ++++++++++++++++++++++++++++++------------------------------
|
|
1 file changed, 31 insertions(+), 30 deletions(-)
|
|
|
|
diff --git a/src/Makefile b/src/Makefile
|
|
index 607ab45..a88adf4 100644
|
|
--- a/src/Makefile
|
|
+++ b/src/Makefile
|
|
@@ -52,15 +52,16 @@ TESTOPTS=
|
|
WINMAKE=mingw32-make
|
|
|
|
LDLIBS = -lm
|
|
-AR = ar
|
|
-CC = gcc
|
|
-CPP = g++
|
|
-O_OPTS = -O2
|
|
-CC_OPTS = -g -Wall -D__USE_FIXED_PROTOTYPES__
|
|
-P_DEFINES =
|
|
+AR ?= ar
|
|
+CC ?= gcc
|
|
+CXX ?= g++
|
|
+O_OPTS ?=
|
|
+CC_OPTS ?= -Wall -D__USE_FIXED_PROTOTYPES__
|
|
+P_DEFINES ?=
|
|
|
|
-CFLAGS = $(CC_OPTS) $(O_OPTS)
|
|
-LDFLAGS = -g
|
|
+CFLAGS += $(CC_OPTS) $(O_OPTS)
|
|
+CXXFLAGS += $(CC_OPTS) $(O_OPTS)
|
|
+LDFLAGS +=
|
|
# Note, for profiling, use
|
|
# make O_OPTS='-pg -O0' LDFLAGS='-g -pg'
|
|
|
|
@@ -92,7 +93,7 @@ LIBPRIMER3 = libprimer3.a
|
|
LIBPRIMER3_DYN = libprimer3.so.1.0.0
|
|
LIBRARIES = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM)
|
|
DYNLIBS = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN)
|
|
-RANLIB = ranlib
|
|
+RANLIB ?= ranlib
|
|
|
|
PRIMER_OBJECTS1=primer3_boulder_main.o\
|
|
format_output.o\
|
|
@@ -127,85 +128,85 @@ $(LIBOLIGOTM): oligotm.o
|
|
$(RANLIB) $@
|
|
|
|
$(LIBOLIGOTM_LIB): oligotm.o
|
|
- $(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
|
|
+ $(CC) $(LDFLAGS) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
|
|
|
|
$(LIBDPAL): dpal_primer.o
|
|
$(AR) rv $@ dpal_primer.o
|
|
$(RANLIB) $@
|
|
|
|
$(LIBDPAL_DYN): dpal_primer.o
|
|
- $(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
|
|
+ $(CC) $(LDFLAGS) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
|
|
|
|
$(LIBTHAL): thal_primer.o
|
|
$(AR) rv $@ thal_primer.o
|
|
$(RANLIB) $@
|
|
|
|
$(LIBTHAL_DYN): thal_primer.o
|
|
- $(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
|
|
+ $(CC) $(LDFLAGS) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
|
|
|
|
$(LIBPRIMER3): libprimer3.o p3_seq_lib.o
|
|
$(AR) rv $@ libprimer3.o p3_seq_lib.o
|
|
$(RANLIB) $@
|
|
|
|
$(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o
|
|
- $(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
|
|
+ $(CC) $(LDFLAGS) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
|
|
|
|
$(PRIMER_EXE): $(PRIMER_OBJECTS)
|
|
- $(CPP) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
|
|
+ $(CXX) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
|
|
|
|
libprimer3.o: libprimer3.c libprimer3.h p3_seq_lib.h dpal.h thal.h oligotm.h
|
|
- $(CPP) -c $(CFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c
|
|
+ $(CXX) -c $(CXXFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c
|
|
|
|
$(NTDPAL_EXE): ntdpal_main.o dpal.o
|
|
- $(CPP) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
|
|
+ $(CXX) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
|
|
|
|
$(NTTHAL_EXE): thal_main.o thal.o
|
|
- $(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
|
|
+ $(CXX) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
|
|
|
|
$(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM)
|
|
- $(CPP) $(CFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
|
|
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
|
|
|
|
$(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o
|
|
- $(CPP) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
|
|
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
|
|
|
|
read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h p3_seq_lib.h
|
|
- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c
|
|
+ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ read_boulder.c
|
|
|
|
print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h
|
|
- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ print_boulder.c
|
|
+ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ print_boulder.c
|
|
|
|
dpal.o: dpal.c dpal.h
|
|
- $(CPP) -c $(CFLAGS) -o $@ dpal.c
|
|
+ $(CXX) -c $(CXXFLAGS) -o $@ dpal.c
|
|
|
|
# We use '-ffloat-store' on windows to prevent undesirable
|
|
# precision which may lead to differences in floating point results.
|
|
thal.o: thal.c thal.h
|
|
- $(CPP) -c $(CFLAGS) -ffloat-store -o $@ thal.c
|
|
+ $(CXX) -c $(CXXFLAGS) -ffloat-store -o $@ thal.c
|
|
|
|
p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h
|
|
- $(CPP) -c $(CFLAGS) -o $@ p3_seq_lib.c
|
|
+ $(CXX) -c $(CXXFLAGS) -o $@ p3_seq_lib.c
|
|
|
|
dpal_primer.o: dpal.c dpal.h
|
|
- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c
|
|
+ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ dpal.c
|
|
|
|
thal_primer.o: thal.c thal.h
|
|
- $(CPP) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
|
|
+ $(CXX) -c $(CXXFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
|
|
|
|
format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h
|
|
- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c
|
|
+ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ format_output.c
|
|
|
|
ntdpal_main.o: ntdpal_main.c dpal.h
|
|
- $(CPP) -c $(CC_OPTS) -o $@ ntdpal_main.c
|
|
+ $(CXX) -c $(CXXFLAGS) -o $@ ntdpal_main.c
|
|
|
|
thal_main.o: thal_main.c thal.h
|
|
- $(CPP) -c $(CFLAGS) -o $@ thal_main.c
|
|
+ $(CXX) -c $(CXXFLAGS) -o $@ thal_main.c
|
|
# We use CC_OPTS above rather than CFLAGS because
|
|
# gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2
|
|
|
|
oligotm.o: oligotm.c oligotm.h
|
|
|
|
primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h oligotm.h format_output.h print_boulder.h read_boulder.h
|
|
- $(CPP) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c
|
|
+ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) primer3_boulder_main.c
|
|
|
|
primer_test: test
|
|
|