File: makefile

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clustalw 1.82-3
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ifndef
  DESTDIR=/
endif
BINDIR=$(DESTDIR)/usr/bin
XBINDIR=$(DESTDIR)/usr/X11R6/bin
DOCDIR=$(DESTDIR)/usr/share/doc/clustalw
XDOCDIR=$(DESTDIR)/usr/share/doc/clustalx
LIBDIR=$(DESTDIR)/usr/share/clustalw
MANDIR=$(DESTDIR)/usr/share/man/man1
XMANDIR=$(DESTDIR)/usr/X11R6/man/man1
DOCS=clustalw.doc clustalw.ms README
XDOCS=README.clustalx clustalx.html

MACHINE=$(shell uname -m)

all: clustalx clustalw

clean:
	rm -f *.o

distclean:
	make clean
	rm -f clustalw clustalx
	cd tests.clustalw; make clean

OBJECTS = interface.o sequence.o showpair.o malign.o \
  	util.o trees.o gcgcheck.o prfalign.o pairalign.o \
  	calcgapcoeff.o calcprf1.o calcprf2.o calctree.o \
        readmat.o alnscore.o random.o 

XOBJECTS = xutils.o xmenu.o xcolor.o xdisplay.o xscore.o

HEADERS = general.h clustalw.h

CC	= cc
ifeq ("$(MACHINE)","alpha")
 # -mieee is for the Alpha only: ClustalW divides by zero (yes, I know it's bad) # and expect the processor to goes on. -mieee tells the Alpha to comply with
 # the IEEE standard and to shut up about divisions by zero.
 CFLAGS  = -c -g -O2 -mieee
else
 CFLAGS  = -c -g -O2
endif
LFLAGS	= -O -lm 
#NCBI_INC  = /dec/biolo/ncbi/include
#NCBI_LIB	= /dec/biolo/ncbi/lib
NCBI_INC  = /usr/include/ncbi
#NCBI_LIB	= /usr/lib
CXFLAGS  = -DWIN_MOTIF -I$(NCBI_INC)
#LXFLAGS	= -L$(NCBI_LIB) -lvibrant -lncbi -lpthread -lXm -lXmu -lXt -lX11 -lm 
LXFLAGS	= -L/usr/X11R6/lib -lvibrant -lncbi -lpthread -lXm -lXmu -lXt -lX11 -lm 

machine:
	echo $(MACHINE)

clustalw : $(OBJECTS) amenu.o clustalw.o
	$(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS)

interface.o : interface.c $(HEADERS) param.h
	$(CC) $(CFLAGS) $*.c

amenu.o : amenu.c $(HEADERS) param.h
	$(CC) $(CFLAGS) $*.c

clustalx : $(OBJECTS) $(XOBJECTS) clustalx.o
	$(CC) -o $@ $(OBJECTS) $(XOBJECTS) clustalx.o $(LFLAGS) $(LXFLAGS)

clustalx.o : clustalx.c $(HEADERS)
	$(CC) $(CFLAGS) $(CXFLAGS) $*.c

xmenu.o : xmenu.c $(HEADERS) param.h
	$(CC) $(CFLAGS) $(CXFLAGS) $*.c

xdisplay.o : xdisplay.c $(HEADERS) param.h
	$(CC) $(CFLAGS) $(CXFLAGS) $*.c

xutils.o : xutils.c $(HEADERS) param.h
	$(CC) $(CFLAGS) $(CXFLAGS) $*.c

xcolor.o : xcolor.c $(HEADERS) param.h
	$(CC) $(CFLAGS) $(CXFLAGS) $*.c

xscore.o : xscore.c $(HEADERS) param.h
	$(CC) $(CFLAGS) $(CXFLAGS) $*.c

readmat.o : readmat.c $(HEADERS) matrices.h
	$(CC) $(CFLAGS) $*.c

trees.o : trees.c $(HEADERS) dayhoff.h
	$(CC) $(CFLAGS) $*.c

.c.o :
	$(CC) $(CFLAGS) $?

install:
	install -d $(BINDIR) $(XBINDIR) $(LIBDIR) $(DOCDIR)/examples $(MANDIR) $(XMANDIR) $(XDOCDIR)
	install -m 0755 clustalw $(BINDIR)
	install -m 0755 clustalx $(XBINDIR)
	install -m 0644 clustalw_help clustalx_help $(LIBDIR)
	install -m 0644 clustalw.1 $(MANDIR)
	install -m 0644 clustalx.1x $(XMANDIR)
	install -m 0644 $(DOCS) $(DOCDIR)
	install -m 0644 $(XDOCS) $(XDOCDIR)
	cp -a -R tests.clustalw $(DOCDIR)/examples/tests