Added bowtie to makefile

Makefile

@@ -1,20 +1,42 @@
 trimmomatic_version := 0.32
 trimmomatic := Trimmomatic-$(trimmomatic_version)
-trimmomatic_dir := lib/$(trimmomatic)/
+trimmomatic_bin := lib/$(trimmomatic)/trimmomatic-$(trimmomatic_version).jar
+
 bismark_version := v0.12.3
 bismark := bismark_$(bismark_version)
-bismark_dir := lib/$(bismark)/
+bismark_bin := lib/$(bismark)/bismark
+
+bowtie_version := 1.1.1
+bowtie := bowtie-$(bowtie_version)-linux-x86_64
+bowtie_bin := lib/bowtie-$(bowtie_version)/bowtie
+
+install: bismark trimmomatic bowtie
+
+bismark: $(bismark_bin)
+
+trimmomatic: $(trimmomatic_bin)
+
+bowtie: $(bowtie_bin)
 
-install: $(bismark_bin) $(trimmomatic_jar)
 
 lib/$(trimmomatic).zip:
-	curl -o $@ http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/$(trimmomatic).zip
+	curl -L -o $@ http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/$(trimmomatic).zip
 
-$(trimmomatic_dir): lib/$(trimmomatic).zip
+$(trimmomatic_bin): lib/$(trimmomatic).zip
 	cd lib; unzip $(<F)
+	touch $@
 
 lib/$(bismark).tar.gz:
-	curl -o $@ http://www.bioinformatics.babraham.ac.uk/projects/bismark/$(bismark).tar.gz
+	curl -L -o $@ http://www.bioinformatics.babraham.ac.uk/projects/bismark/$(bismark).tar.gz
 
-$(bismark_dir): lib/$(bismark).tar.gz
+$(bismark_bin): lib/$(bismark).tar.gz
 	cd lib; tar -xzf $(<F)
+	touch $@
+
+
+lib/$(bowtie).zip:
+	curl -L -o $@ http://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.1.1/$(bowtie).zip
+
+$(bowtie_bin): lib/$(bowtie).zip
+	cd lib; unzip $(<F)
+	touch $@