From 422582bc055d6cc7ca1a61ff8345defccbc6058a Mon Sep 17 00:00:00 2001
From: Angel Pizarro
Date: Fri, 13 Apr 2012 11:37:01 -0400
Subject: GMAP/GSNAP 2012-04-10

GMAP/GSNAP is a widely used tool for alignment of high-throughput sequence data.
See details about GMAP/GSNAP here:
http://research-pub.gene.com/gmap

Here is the referencable peer-reviewed paper:

Thomas D. Wu and Colin K. Watanabe
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Bioinformatics 2005 21:1859-1875

PUBMED ID 15728110 full citation at http://www.ncbi.nlm.nih.gov/pubmed/15728110

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
---
 Library/Formula/gmap-gsnap.rb | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 Library/Formula/gmap-gsnap.rb

diff --git a/Library/Formula/gmap-gsnap.rb b/Library/Formula/gmap-gsnap.rb
new file mode 100644
index 000000000..84dca2a2e
--- /dev/null
+++ b/Library/Formula/gmap-gsnap.rb
@@ -0,0 +1,31 @@
+require 'formula'
+
+class GmapGsnap < Formula
+  homepage 'http://research-pub.gene.com/gmap'
+  url 'http://research-pub.gene.com/gmap/src/gmap-gsnap-2012-04-10.tar.gz'
+  md5 'acd1731524eb3517f6e82147c646d27d'
+  version "2012-04-10"
+
+  depends_on "samtools"
+
+  def install
+    ENV['CC'] = "#{ENV.cc} -O3 -m#{MacOS.prefer_64_bit? ? 64 : 32}"
+    system "./configure", "--prefix=#{prefix}"
+    system "make"
+    system "make install"
+  end
+
+  def caveats; <<-EOF.undent
+    You will need to either download or build indexed search databases.
+    See the readme file for how to do this:
+      http://research-pub.gene.com/gmap/src/README
+
+    Databases will be installed to:
+      #{share}
+    EOF
+  end
+
+  def test
+    system "#{bin}/gsnap --version"
+  end
+end
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