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Makefile
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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