PATH2SCAFFOLDER	= /home/lmsalmel/mip-scaffolder-0.5/
LEMONROOT	= /home/lmsalmel/lemon/
LPSOLVEROOT	= /home/lmsalmel/lp-solve/


PROG		= mip-scaffolder
VERSION		= 0.5

SUBDIRS		= scripts common filter-mappings split-scaffold \
		combine-scaffold write-scaffold

all:
		@for i in $(SUBDIRS); do \
		(cd $$i; make PATH2SCAFFOLDER=$(PATH2SCAFFOLDER) LEMONROOT=$(LEMONROOT) LPSOLVEROOT=$(LPSOLVEROOT)); done

dist:
		mkdir $(PROG)-$(VERSION)
		mkdir $(PROG)-$(VERSION)/scripts
		mkdir $(PROG)-$(VERSION)/common
		mkdir $(PROG)-$(VERSION)/filter-mappings
		mkdir $(PROG)-$(VERSION)/split-scaffold
		mkdir $(PROG)-$(VERSION)/combine-scaffold
		mkdir $(PROG)-$(VERSION)/write-scaffold

		cp scripts/Makefile $(PROG)-$(VERSION)/scripts
		cp scripts/filter-mappings.stub $(PROG)-$(VERSION)/scripts
		cp scripts/merge.stub $(PROG)-$(VERSION)/scripts
		cp scripts/mip-scaffolder.plstub $(PROG)-$(VERSION)/scripts
		cp scripts/merge-mapping-lines.pl $(PROG)-$(VERSION)/scripts
		cp scripts/translate-depth.pl $(PROG)-$(VERSION)/scripts
		cp scripts/translate-mappings.pl $(PROG)-$(VERSION)/scripts

		cp common/Makefile $(PROG)-$(VERSION)/common
		cp common/*.cpp $(PROG)-$(VERSION)/common
		cp common/*.h $(PROG)-$(VERSION)/common

		cp filter-mappings/Makefile $(PROG)-$(VERSION)/filter-mappings
		cp filter-mappings/*.cpp $(PROG)-$(VERSION)/filter-mappings

		cp split-scaffold/Makefile $(PROG)-$(VERSION)/split-scaffold
		cp split-scaffold/*.cpp $(PROG)-$(VERSION)/split-scaffold
		cp split-scaffold/*.h $(PROG)-$(VERSION)/split-scaffold

		cp combine-scaffold/Makefile $(PROG)-$(VERSION)/combine-scaffold
		cp combine-scaffold/*.cpp $(PROG)-$(VERSION)/combine-scaffold
		cp combine-scaffold/*.h $(PROG)-$(VERSION)/combine-scaffold

		cp write-scaffold/Makefile  $(PROG)-$(VERSION)/write-scaffold
		cp write-scaffold/*.cpp  $(PROG)-$(VERSION)/write-scaffold
		cp write-scaffold/*.h  $(PROG)-$(VERSION)/write-scaffold

		sed 's/VERSION/$(VERSION)/g' < README > $(PROG)-$(VERSION)/README
		cp COPYING $(PROG)-$(VERSION)/
		cp Makefile $(PROG)-$(VERSION)/
		tar zcvf $(PROG)-$(VERSION).tar.gz $(PROG)-$(VERSION)

dist-clean:
		rm -r $(PROG)-$(VERSION)/
