Miscellany

#
# Invoking this makefile with JOB set will pass that as the item to make onto
# all sublevel makefiles. eg "gmake JOB=clean".
#

include	 system.mk

DIRS =	Misc\
	tk_utils\
	text_utils\
	seq_utils\
	mutlib\
	abi\
	alf\
	g\
	trev\
	primer3\
	primer3/src\
	gap4\
	prefinish\
	haplo\
	eba\
	init_exp\
	get_scf_field\
	spin\
	vector_clip\
	tracediff\
	screen_seq\
	qclip\
	polyA_clip\
	stops\
	pregap4\
	make_weights\
	find_renz\
	spin_emboss\
	copy_reads\
	hetins\
	mutscan\
	convert\
	tgap\
	gap5\
	scripts\
	data

JOB = all

all:	$(DIRS)

clean:
	$(MAKE) $(FLAGS) JOB=clean

%.clean:
	$(MAKE) $* $(FLAGS) JOB=clean

spotless:
	$(MAKE) $(FLAGS) JOB=spotless

relink:
	$(MAKE) $(FLAGS) JOB=relink

%.relink:
	$(MAKE) $* $(FLAGS) JOB=relink

depend:
	$(MAKE) $(FLAGS) JOB=depend

%.depend:
	$(MAKE) $* $(FLAGS) JOB=depend

# Installs newly built executables into $STADENROOT/$(MACHINE)-bin
# FIXME:
install:
	-mkdir -p $(INSTALLLIB)
	-mkdir -p $(INSTALLBIN)
	-mkdir -p $(INSTALLETC)
	-mkdir -p $(INSTALLSHARE)
	-mkdir -p $(INSTALLSCRIPTS)
	-mkdir -p $(INSTALLTCL)
	-mkdir -p $(INSTALLDOC)
	-mkdir -p $(INSTALLMAN)
	cp shlib.conf $(INSTALLETC)
	cp ./staden.profile $(INSTALLSHARE)
	$(MAKE) $(FLAGS) JOB=install


.PHONY: distcommon distwindows distunix


# Full source is available now, so we no longer need to copy any of this
# when building a binary distribution.

# Make install does most of the work, but this doesn't install the third
# party libraries. So we'll do that here. NOTE: this only installs the
# binary components. The tcl/itcl files are already in the ../lib directory
# and will be copied over separately. This is because in some cases they will
# have been manually hacked/bug fixed.
distunix:
	-mkdir $(DIST)/lib/$(MACHINE)-binaries 
	-cp -R lib/$(MACHINE)-binaries/libpng* $(DIST)/lib/$(MACHINE)-binaries
	-cp -R lib/$(MACHINE)-binaries/libtcl* $(DIST)/lib/$(MACHINE)-binaries
	-cp -R lib/$(MACHINE)-binaries/libtk* $(DIST)/lib/$(MACHINE)-binaries
	-cp -R lib/$(MACHINE)-binaries/libitcl* $(DIST)/lib/$(MACHINE)-binaries
	-cp -R lib/$(MACHINE)-binaries/libitk* $(DIST)/lib/$(MACHINE)-binaries


distwindows:
	-mkdir $(DIST)/lib/windows-binaries 
	-cp lib/windows-binaries/* $(DIST)/lib/windows-binaries
	-cp windows/run/sprun.exe $(DIST)/windows-bin/
	-cp windows/run/sprun.exe $(DIST)/windows-bin/gap.exe
	-cp windows/run/sprun.exe $(DIST)/windows-bin/pregap4.exe
	-cp windows/run/sprun.exe $(DIST)/windows-bin/spin.exe
	-cp windows/run/sprun.exe $(DIST)/windows-bin/trev.exe
	-cp tk8.4.6/win/wish84.exe $(DIST)/windows-bin/wish.exe
	#-cp trev/trev.bat $(DIST)/windows-bin
	#-cp gap4/gap4.bat $(DIST)/windows-bin
	#-cp spin/spin.bat $(DIST)/windows-bin
	#-cp pregap4/pregap4.bat $(DIST)/windows-bin
	-cp ../windows-bin/*.exe $(DIST)/windows-bin
	$(MAKE) STADENROOT=$(DIST) MACHINE=windows install
	-rm $(DIST)/windows-bin/gap4
	-rm $(DIST)/windows-bin/spin
	-rm $(DIST)/windows-bin/trev
	-rm $(DIST)/windows-bin/pregap4
	-rm $(DIST)/windows-bin/assemble4
	-rm $(DIST)/windows-bin/finish_sanger



DS=staden-2.0.0b6-src
S=$(SRCROOT)
distsrc:
#
#	General souce. Works best from a clean svn checkout.
	-mkdir $(DS)
	cp $(S)/configure $(S)/*.in $(S)/bootstrap $(S)/README.build \
	   $(S)/NEWS $(S)/ChangeLog $(S)/global.mk $(S)/staden.profile $(DS)
	-mkdir $(DS)/ac_stubs
	cp $(S)/ac_stubs/*.m4 $(DS)/ac_stubs
#
#	Recurse through sub-directories too
	$(MAKE) $(FLAGS) DISTSRC=$(PWD)/$(DS) JOB=distsrc
	chmod -R go-w $(DS)
#
#	 Windows compilation bits
#	-mkdir $(S)/windows
#	cp -R windows/include $(S)
#	-mkdir $(S)/mkdef
#	cp -R windows/mkdef/mkdef.* $(S)/mkdef
#	-mkdir $(S)/run
#	cp -R windows/run/run.* \
#	      windows/run/main.cpp\
#	      windows/run/notes.txt\
#	      windows/run/sprun.rc\
#	      windows/run/staden.ico\
#	      $(S)/run
#	mkdir $(S)/windows/dumpenv
#	cp -R windows/dumpenv/dumpenv.*\
#	      windows/dumpenv/main.cpp\
#	      $(S)/windows/dumpenv
#	mkdir $(S)/windows/stashmsg
#	cp -R windows/stashmsg/stashmsg.*\
#	      windows/stashmsg/icon1.ico\
#	      windows/stashmsg/messages.*\
#	      windows/stashmsg/msg00001.bin\
#	      windows/stashmsg/resource.h\
#	      windows/stashmsg/stadenmsg.rc\
#	      $(S)/windows/stashmsg
#	cp -R windows/install-2003 $(S)/windows

$(DIRS): FORCE
	@if ! test -f $@/.dir; \
	then \
	    mkdir -p $@; \
	    cd $@; \
	    touch .dir; \
	fi

	cd $@ && $(MAKE) -f $(SRCROOT)/$@/Makefile $(FLAGS) $(MFLAGS) BUILD=$(PWD) SRC=$(SRCROOT)/$@ SUBDIR=$@ $(JOB)

%/: %
	#

# dependencies so e.g. make -j4 works.
tk_utils: Misc
text_utils: Misc
seq_utils: Misc text_utils tk_utils
mutlib: Misc seq_utils
abi: Misc
alf: Misc
eba: Misc
get_scf_field: Misc
hetins: Misc
init_exp: Misc
find_renz: seq_utils
make_weights: seq_utils
polyA_clip: seq_utils
qclip: seq_utils
screen_seq: seq_utils
stops: seq_utils
vector_clip: seq_utils
mutscan: mutlib
tracediff: mutlib
spin: seq_utils
g: Misc
gap4: g seq_utils mutlib primer3/src
convert: gap4
copy_reads: gap4
haplo: gap4
prefinish: gap4
tgap: seq_utils
gap5: tgap

FORCE:
# DO NOT DELETE THIS LINE -- make depend depends on it.