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Makefile
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PREFIX = /usr/local
LIBDIR = $(PREFIX)/libexec/mafft
BINDIR = $(PREFIX)/bin
DESTDIR =
#MNO_CYGWIN = -mno-cygwin
ENABLE_MULTITHREAD = -Denablemultithread
# Comment out the above line if your compiler
# does not support TLS (thread-local strage).
#ENABLE_ATOMIC = -Denableatomic
# Comment out the above line if your compiler
# does not support "atomic_int".
CC = gcc
#CC = icc
CFLAGS = -g -O3 -D _GNU_SOURCE -m64 -static
#CFLAGS = -O3 -fPIC
# add -fPIC when building .so files
#CC = icc
#CFLAGS = -fast
# if you have icc, use this.
ifdef ENABLE_MULTITHREAD
LIBS = -lm -lpthread
else
LIBS = -lm
endif
ifdef ENABLE_ATOMIC
STDF = -std=c11
else
STDF = -std=c99
endif
MYCFLAGS = $(MNO_CYGWIN) $(ENABLE_MULTITHREAD) $(ENABLE_ATOMIC) $(STDF) $(CFLAGS)
INSTALL = install
STRIP = strip
#STRIP = true # to disable strip
PROGS = staralign profilealign fragalign profile_two_align
OBJALIGN = mtxutl.o io.o mltaln9.o tddis.o constants.o Falign.o Galign11.o SAalignmm.o \
defs.o fft.o fftFunctions.o Salignmm.o Kband.o
OBJSTARALIGN = $(OBJALIGN) staralign.o $(MULTIOBJ)
OBJPROFILEALIGN = $(OBJALIGN) profilealign.o $(MULTIOBJ)
OBJFRAGALIGN = $(OBJALIGN) fragalign.o $(MULTIOBJ)
OBJ2PROFILEALIGN = $(OBJALIGN) profile_two_align.o
ifdef ENABLE_MULTITHREAD
MULTIOBJ = threadpool.o threadpool_condition.o
endif
HEADER = mltaln.h mtxutl.h version.h
ifdef ENABLE_MULTITHREAD
MULTIHEADER = threadpool.h threadpool_condition.h
endif
FFTHEADER = fft.h
KBANDHEADER = Kband.h
all : $(PROGS) $(SCRIPTS)
@echo done.
mltaln.h : functions.h
touch mltaln.h
staralign: $(OBJSTARALIGN)
$(CC) -o $@ $(OBJSTARALIGN) $(MYCFLAGS) $(LDFLAGS) $(LIBS)
profilealign: $(OBJPROFILEALIGN)
$(CC) -o $@ $(OBJPROFILEALIGN) $(MYCFLAGS) $(LDFLAGS) $(LIBS)
fragalign: $(OBJFRAGALIGN)
$(CC) -o $@ $(OBJFRAGALIGN) $(MYCFLAGS) $(LDFLAGS) $(LIBS)
profile_two_align: $(OBJ2PROFILEALIGN)
$(CC) -o $@ $(OBJ2PROFILEALIGN) $(MYCFLAGS) $(LDFLAGS) $(LIBS)
mltaln9.o : mltaln9.c $(HEADER)
$(CC) $(MYCFLAGS) -c mltaln9.c
tddis.o : tddis.c $(HEADER)
$(CC) $(MYCFLAGS) -c tddis.c
constants.o : constants.c miyata.h miyata5.h blosum.c DNA.h JTT.c $(HEADER)
$(CC) $(MYCFLAGS) -c constants.c
defs.o : defs.c
$(CC) $(MYCFLAGS) -c defs.c
Salignmm.o : Salignmm.c $(HEADER)
$(CC) $(MYCFLAGS) -c Salignmm.c
Galign11.o : Galign11.c $(HEADER)
$(CC) $(MYCFLAGS) -c Galign11.c
SAalignmm.o : SAalignmm.c $(HEADER)
$(CC) $(MYCFLAGS) -c SAalignmm.c -o SAalignmm.o
disttbfast.o : disttbfast.c $(HEADER) $(FFTHEADER)
$(CC) $(MYCFLAGS) -c disttbfast.c
staralign.o : staralign.c $(HEADER) $(FFTHEADER) $(MULTIHEADER)
$(CC) $(MYCFLAGS) -c staralign.c
profilealign.o : profilealign.c $(HEADER) $(FFTHEADER) $(MULTIHEADER)
$(CC) $(MYCFLAGS) -c profilealign.c
profile_two_align.o: profile_two_align.c $(HEADER) $(FFTHEADER) $(MULTIHEADER)
$(CC) $(MYCFLAGS) -c profile_two_align.c
fragalign.o : fragalign.c $(HEADER) $(FFTHEADER) $(MULTIHEADER)
$(CC) $(MYCFLAGS) -c fragalign.c
threadpool_condition.o : threadpool_condition.c $(HEADER) $(MULTIHEADER)
$(CC) $(MYCFLAGS) -c threadpool_condition.c
threadpool.o : threadpool.c $(HEADER) $(MULTIHEADER)
$(CC) $(MYCFLAGS) -c threadpool.c
io.o : io.c $(HEADER) $(FFTHEADER)
$(CC) $(MYCFLAGS) -c io.c
fft.o : fft.c $(HEADER) $(FFTHEADER)
$(CC) $(MYCFLAGS) -c fft.c
fftFunctions.o : fftFunctions.c $(HEADER) $(FFTHEADER)
$(CC) $(MYCFLAGS) -c fftFunctions.c
Falign.o : Falign.c $(HEADER) $(FFTHEADER) $(MTXHEADER)
$(CC) $(MYCFLAGS) -c Falign.c
mtxutl.o : mtxutl.c
$(CC) $(MYCFLAGS) -c mtxutl.c
addfunctions.o : addfunctions.c $(HEADER)
$(CC) $(MYCFLAGS) -c addfunctions.c
Kband.o : Kband.c $(KBANDHEADER)
$(CC) $(MYCFLAGS) -c Kband.c
clean :
rm -f *.o *.a *.exe *~ $(PROGS) $(SOS) $(DYLIBS) $(DLLS) *.gcda *.gcno $(DASH_CLIENT) pre trace *.aps
# rm -f ../binaries/* ../scripts/*
install : all
mkdir -p $(DESTDIR)$(LIBDIR)
chmod 755 $(DESTDIR)$(LIBDIR)
mkdir -p $(DESTDIR)$(BINDIR)
chmod 755 $(DESTDIR)$(BINDIR)
chmod 755 $(SCRIPTS)
chmod 755 $(PROGS) ||: # in MinGW, it's ok if this fails
$(STRIP) $(PROGS) ||: # may fail for dash_client on mac.
$(INSTALL) $(PROGS) $(DESTDIR)$(LIBDIR)