From 4c6bc7bcb9438e8e02c4ec448776ad450800fe5d Mon Sep 17 00:00:00 2001
From: Lance Parsons
Date: Fri, 20 Jan 2012 18:53:34 -0500
Subject: New formula: fastx_toolkit

The FASTX-Toolkit is a collection of command line tools for Short-Reads
FASTA/FASTQ files preprocessing that are well suited for processing High
Throughput Sequencing data

Closes #9697.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
---
 Library/Formula/fastx_toolkit.rb | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 Library/Formula/fastx_toolkit.rb

(limited to 'Library/Formula')

diff --git a/Library/Formula/fastx_toolkit.rb b/Library/Formula/fastx_toolkit.rb
new file mode 100644
index 000000000..21c627c93
--- /dev/null
+++ b/Library/Formula/fastx_toolkit.rb
@@ -0,0 +1,32 @@
+require 'formula'
+
+class FastxToolkit < Formula
+  homepage 'http://hannonlab.cshl.edu/fastx_toolkit/'
+  url 'http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit-0.0.13.tar.bz2'
+  md5 '6d233ff4ae3d52c457d447179f073a56'
+
+  depends_on 'pkg-config' => :build
+  depends_on 'libgtextutils'
+
+  def install
+    system "./configure", "--disable-debug",
+                          "--disable-dependency-tracking",
+                          "--prefix=#{prefix}"
+    system "make install"
+  end
+
+  def test
+    fixture = <<-EOS.undent
+      >MY-ID
+      AAAAAGGGGG
+      CCCCCTTTTT
+      AGCTN
+      EOS
+    expect = <<-EOS.undent
+      >MY-ID
+      AAAAAGGGGGCCCCCTTTTTAGCTN
+      EOS
+    actual = `echo "#{fixture}" | #{bin}/fasta_formatter`
+    actual == expect
+  end
+end
-- 
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