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all: doc bin package



CROSSBOW_VERSION=$(shell cat VERSION)

SF_BOWTIE_BASE=https://sourceforge.net/projects/bowtie-bio/files/bowtie

SF_BOWTIE_MID=

BOWTIE_VERSION=0.12.8

MACOS_VERSION=10.6



doc: doc/manual.html MANUAL

.PHONY: doc



doc/manual.html: MANUAL.markdown

	echo "<h1>Table of Contents</h1>" > .tmp.head

	pandoc -T "Crossbow $(CROSSBOW_VERSION) Manual" -B .tmp.head \

	       --css style.css -o $@ \

	       --from markdown --to HTML \

	       --table-of-contents $^



MANUAL: MANUAL.markdown

	perl doc/strip_markdown.pl < $^ > $@



.PHONY: bin32

bin32: bin/linux32/bowtie \

       bin/linux32/bowtie-build \

       bin/linux32/bowtie-debug \

       bin/linux32/bowtie-build-debug \

       bin/linux32/soapsnp \

       bin/linux32/soapsnp-debug \

       bin/mac32/bowtie \

       bin/mac32/bowtie-build \

       bin/mac32/bowtie-debug \

       bin/mac32/bowtie-build-debug \

       bin/mac32/soapsnp \

       bin/mac32/soapsnp-debug



.PHONY: bin64

bin64: bin/linux64/bowtie \

       bin/linux64/bowtie-build \

       bin/linux64/bowtie-debug \

       bin/linux64/bowtie-build-debug \

       bin/linux64/soapsnp \

       bin/linux64/soapsnp-debug \

       bin/mac64/bowtie \

       bin/mac64/bowtie-build \

       bin/mac64/bowtie-debug \

       bin/mac64/bowtie-build-debug \

       bin/mac64/soapsnp \

       bin/mac64/soapsnp-debug



.PHONY: bin

bin: bin64



#bin/linux32/bowtie: bowtie-$(BOWTIE_VERSION)-linux-i386.zip

#	mkdir -p bin/linux32

#	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie

#	mv bowtie-$(BOWTIE_VERSION)/bowtie $@

#	rm -rf bowtie-$(BOWTIE_VERSION)



#bin/linux32/bowtie-build: bowtie-$(BOWTIE_VERSION)-linux-i386.zip

#	mkdir -p bin/linux32

#	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie-build

#	mv bowtie-$(BOWTIE_VERSION)/bowtie-build $@

#	rm -rf bowtie-$(BOWTIE_VERSION)



#bin/linux32/bowtie-debug: bowtie-$(BOWTIE_VERSION)-linux-i386.zip

#	mkdir -p bin/linux32

#	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie-debug

#	mv bowtie-$(BOWTIE_VERSION)/bowtie-debug $@

#	rm -rf bowtie-$(BOWTIE_VERSION)



#bin/linux32/bowtie-build-debug: bowtie-$(BOWTIE_VERSION)-linux-i386.zip

#	mkdir -p bin/linux32

#	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie-build-debug

#	mv bowtie-$(BOWTIE_VERSION)/bowtie-build-debug $@

#	rm -rf bowtie-$(BOWTIE_VERSION)





bin/linux64/bowtie: bowtie-$(BOWTIE_VERSION)-linux-x86_64.zip

	mkdir -p bin/linux64

	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie

	mv bowtie-$(BOWTIE_VERSION)/bowtie $@

	rm -rf bowtie-$(BOWTIE_VERSION)



bin/linux64/bowtie-build: bowtie-$(BOWTIE_VERSION)-linux-x86_64.zip

	mkdir -p bin/linux64

	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie-build

	mv bowtie-$(BOWTIE_VERSION)/bowtie-build $@

	rm -rf bowtie-$(BOWTIE_VERSION)



bin/linux64/bowtie-debug: bowtie-$(BOWTIE_VERSION)-linux-x86_64.zip

	mkdir -p bin/linux64

	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie-debug

	mv bowtie-$(BOWTIE_VERSION)/bowtie-debug $@

	rm -rf bowtie-$(BOWTIE_VERSION)



bin/linux64/bowtie-build-debug: bowtie-$(BOWTIE_VERSION)-linux-x86_64.zip

	mkdir -p bin/linux64

	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie-build-debug

	mv bowtie-$(BOWTIE_VERSION)/bowtie-build-debug $@

	rm -rf bowtie-$(BOWTIE_VERSION)





#bin/mac32/bowtie: bowtie-$(BOWTIE_VERSION)-macos-$(MACOS_VERSION)-i386.zip

#	mkdir -p bin/mac32

#	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie

#	mv bowtie-$(BOWTIE_VERSION)/bowtie $@

#	rm -rf bowtie-$(BOWTIE_VERSION)



#bin/mac32/bowtie-build: bowtie-$(BOWTIE_VERSION)-macos-$(MACOS_VERSION)-i386.zip

#	mkdir -p bin/mac32

#	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie-build

#	mv bowtie-$(BOWTIE_VERSION)/bowtie-build $@

#	rm -rf bowtie-$(BOWTIE_VERSION)



#bin/mac32/bowtie-debug: bowtie-$(BOWTIE_VERSION)-macos-$(MACOS_VERSION)-i386.zip

#	mkdir -p bin/mac32

#	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie-debug

#	mv bowtie-$(BOWTIE_VERSION)/bowtie-debug $@

#	rm -rf bowtie-$(BOWTIE_VERSION)



#bin/mac32/bowtie-build-debug: bowtie-$(BOWTIE_VERSION)-macos-$(MACOS_VERSION)-i386.zip

#	mkdir -p bin/mac32

#	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie-build-debug

#	mv bowtie-$(BOWTIE_VERSION)/bowtie-build-debug $@

#	rm -rf bowtie-$(BOWTIE_VERSION)





bin/mac64/bowtie: bowtie-$(BOWTIE_VERSION)-macos-$(MACOS_VERSION)-x86_64.zip

	mkdir -p bin/mac64

	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie

	mv bowtie-$(BOWTIE_VERSION)/bowtie $@

	rm -rf bowtie-$(BOWTIE_VERSION)



bin/mac64/bowtie-build: bowtie-$(BOWTIE_VERSION)-macos-$(MACOS_VERSION)-x86_64.zip

	mkdir -p bin/mac64

	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie-build

	mv bowtie-$(BOWTIE_VERSION)/bowtie-build $@

	rm -rf bowtie-$(BOWTIE_VERSION)



bin/mac64/bowtie-debug: bowtie-$(BOWTIE_VERSION)-macos-$(MACOS_VERSION)-x86_64.zip

	mkdir -p bin/mac64

	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie-debug

	mv bowtie-$(BOWTIE_VERSION)/bowtie-debug $@

	rm -rf bowtie-$(BOWTIE_VERSION)



bin/mac64/bowtie-build-debug: bowtie-$(BOWTIE_VERSION)-macos-$(MACOS_VERSION)-x86_64.zip

	mkdir -p bin/mac64

	unzip $^ bowtie-$(BOWTIE_VERSION)/bowtie-build-debug

	mv bowtie-$(BOWTIE_VERSION)/bowtie-build-debug $@

	rm -rf bowtie-$(BOWTIE_VERSION)





bowtie-$(BOWTIE_VERSION)-macos-$(MACOS_VERSION)-i386.zip:

	wget --no-check-certificate $(SF_BOWTIE_BASE)$(SF_BOWTIE_MID)/$(BOWTIE_VERSION)/bowtie-$(BOWTIE_VERSION)-macos-$(MACOS_VERSION)-i386.zip/download



bowtie-$(BOWTIE_VERSION)-macos-$(MACOS_VERSION)-x86_64.zip:

	wget --no-check-certificate $(SF_BOWTIE_BASE)$(SF_BOWTIE_MID)/$(BOWTIE_VERSION)/bowtie-$(BOWTIE_VERSION)-macos-$(MACOS_VERSION)-x86_64.zip/download



bowtie-$(BOWTIE_VERSION)-linux-i386.zip:

	wget --no-check-certificate $(SF_BOWTIE_BASE)$(SF_BOWTIE_MID)/$(BOWTIE_VERSION)/bowtie-$(BOWTIE_VERSION)-linux-i386.zip/download



bowtie-$(BOWTIE_VERSION)-linux-x86_64.zip:

	wget --no-check-certificate $(SF_BOWTIE_BASE)$(SF_BOWTIE_MID)/$(BOWTIE_VERSION)/bowtie-$(BOWTIE_VERSION)-linux-x86_64.zip/download



.PHONY: package

package: bin

	bash util/package.bash