Updated to bowtie v1.0.0. and updated the macos package names accordi…

…ngly.

Makefile

@@ -3,7 +3,7 @@ all: doc bin package
 MYRNA_VERSION=$(shell cat VERSION)
 SF_BOWTIE_BASE=https://sourceforge.net/projects/bowtie-bio/files/bowtie
 SF_BOWTIE_MID=
-BOWTIE_VERSION=0.12.8
+BOWTIE_VERSION=1.0.0
 MACOS_VERSION=10.6
 
 doc: doc/manual.html MANUAL
@@ -87,61 +87,61 @@ bin/linux64/bowtie-build-debug: bowtie-$(BOWTIE_VERSION)-linux-x86_64.zip
 	rm -rf bowtie-$(BOWTIE_VERSION)
 
 
-bin/mac32/bowtie: bowtie-$(BOWTIE_VERSION)-macos-$(MACOS_VERSION)-i386.zip
+bin/mac32/bowtie: bowtie-$(BOWTIE_VERSION)-macos-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
+bin/mac32/bowtie-build: bowtie-$(BOWTIE_VERSION)-macos-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
+bin/mac32/bowtie-debug: bowtie-$(BOWTIE_VERSION)-macos-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
+bin/mac32/bowtie-build-debug: bowtie-$(BOWTIE_VERSION)-macos-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
+bin/mac64/bowtie: bowtie-$(BOWTIE_VERSION)-macos-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
+bin/mac64/bowtie-build: bowtie-$(BOWTIE_VERSION)-macos-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
+bin/mac64/bowtie-debug: bowtie-$(BOWTIE_VERSION)-macos-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
+bin/mac64/bowtie-build-debug: bowtie-$(BOWTIE_VERSION)-macos-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-i386.zip:
+	wget --no-check-certificate $(SF_BOWTIE_BASE)$(SF_BOWTIE_MID)/$(BOWTIE_VERSION)/bowtie-$(BOWTIE_VERSION)-macos-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)-macos-x86_64.zip:
+	wget --no-check-certificate $(SF_BOWTIE_BASE)$(SF_BOWTIE_MID)/$(BOWTIE_VERSION)/bowtie-$(BOWTIE_VERSION)-macos-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