From dd8bb6a40893b7ca300cee82d6074f942326ff3e Mon Sep 17 00:00:00 2001
From: Carlos Borroto <carlos.borroto@gmail.com>
Date: Mon, 7 Mar 2011 15:11:19 -0500
Subject: [PATCH] tophat 1.2.0

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
---
 Formula/tophat.rb | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 Formula/tophat.rb

diff --git a/Formula/tophat.rb b/Formula/tophat.rb
new file mode 100644
index 0000000000..72101c6a5c
--- /dev/null
+++ b/Formula/tophat.rb
@@ -0,0 +1,19 @@
+require 'formula'
+
+class Tophat <Formula
+  url 'http://tophat.cbcb.umd.edu/downloads/tophat-1.2.0.tar.gz'
+  homepage 'http://tophat.cbcb.umd.edu/'
+  md5 '7ada78bdb9a84e13392418aa6cc9142c'
+
+  depends_on 'samtools'
+
+  def install
+    # It seems this project Makefile doesn't like -j4
+    # Disable until consult with upstream
+    ENV.deparallelize
+
+    system "./configure", "--disable-debug", "--disable-dependency-tracking",
+                          "--prefix=#{prefix}"
+    system "make install"
+  end
+end