# MAFFT for ARB
# by Arne Boeckmann (2013)

PROG  = MAFFT

export CC = $(A_CC)

MAFFTDIR=mafft-7.055-with-extensions
SCRIPTDIR=$(MAFFTDIR)/scripts
BINDIR=$(MAFFTDIR)/binaries

MAKEMAFFTCORE := $(MAKE) -C $(MAFFTDIR)/core
MAKEMAFFTEXT  := $(MAKE) -C $(MAFFTDIR)/extensions

# ARBs standard target
$(MAIN) : $(SCRIPTDIR) $(BINDIR)
	$(MAKE) mafft.stamp

%.sync: # sync output - see ../../Makefile@sync
	@( export ID=$$$$; LANG=C; \
	(( $(MAKE) $(@F:.sync=.nosync)) >$(@F).$$ID.log 2>&1 && \
		(cat $(@F).$$ID.log;rm $(@F).$$ID.log)) || (cat $(@F).$$ID.log;rm $(@F).$$ID.log;false))

$(SCRIPTDIR):
	mkdir -p $@

$(BINDIR):
	mkdir -p $@

clean_core: clean_core.sync
clean_core.nosync:
	+$(MAKEMAFFTCORE) clean

clean_extensions: clean_extensions.sync
clean_extensions.nosync:
	+$(MAKEMAFFTEXT) clean

clean_here:
	rm -rf $(ARBHOME)/lib/mafft
	rm -f mafft.stamp
	rm -f $(ARBHOME)/bin/mafft*

clean_dirs:
	rm -rf $(SCRIPTDIR)
	rm -rf $(BINDIR)

clean: clean_core clean_extensions clean_here clean_dirs

make_core : make_core.sync
make_core.nosync:
	+$(MAKEMAFFTCORE)

make_extensions : make_extensions.sync
make_extensions.nosync:
	+$(MAKEMAFFTEXT)

install_core: make_core
	$(MAKE) install_core.sync
install_core.nosync:
	+$(MAKEMAFFTCORE) install

install_extensions: install_core make_extensions
	$(MAKE) install_extensions.sync
install_extensions.nosync:
	+$(MAKEMAFFTEXT) install

mafft.stamp: install_extensions
	touch mafft.stamp

.PHONY : clean clean_core clean_extensions clean_here make_core make_extensions