From c1e5f448e97c08af2ea6bae356258ea0a81ee462 Mon Sep 17 00:00:00 2001
From: Orion Buske <buske@cs.toronto.edu>
Date: Fri, 7 Nov 2014 02:04:04 -0500
Subject: [PATCH] Adding makefile to get necessary programs

---
 Makefile | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 Makefile

diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..aa2beae
--- /dev/null
+++ b/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)