Adding makefile to get necessary programs

Makefile

@@ -0,0 +1,20 @@
+trimmomatic_version := 0.32
+trimmomatic := Trimmomatic-$(trimmomatic_version)
+trimmomatic_dir := lib/$(trimmomatic)/
+bismark_version := v0.12.3
+bismark := bismark_$(bismark_version)
+bismark_dir := lib/$(bismark)/
+
+install: $(bismark_bin) $(trimmomatic_jar)
+
+lib/$(trimmomatic).zip:
+	curl -o $@ http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/$(trimmomatic).zip
+
+$(trimmomatic_dir): lib/$(trimmomatic).zip
+	cd lib; unzip $(<F)
+
+lib/$(bismark).tar.gz:
+	curl -o $@ http://www.bioinformatics.babraham.ac.uk/projects/bismark/$(bismark).tar.gz
+
+$(bismark_dir): lib/$(bismark).tar.gz
+	cd lib; tar -xzf $(<F)