ABySS 1.3.3

Closes Homebrew/homebrew#11884.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>

Formula/abyss.rb

@@ -2,8 +2,9 @@ require 'formula'
 
 class Abyss < Formula
   homepage 'http://www.bcgsc.ca/platform/bioinfo/software/abyss'
-  url 'http://www.bcgsc.ca/downloads/abyss/abyss-1.3.2.tar.gz'
+  url 'http://www.bcgsc.ca/downloads/abyss/abyss-1.3.3.tar.gz'
-  md5 'a7551c95f33a0c61cab50bc35db347e4'
+  md5 '15953363d4ef5795d3a82d129e4ca240'
+  head 'https://github.com/sjackman/abyss.git'
 
   # Only header files are used from these packages, so :build is appropriate
   depends_on 'boost' => :build
@@ -15,13 +16,6 @@ class Abyss < Formula
   # strip breaks the ability to read compressed files.
   skip_clean 'bin'
 
-  # abyss-overlap does not build with LLVM-GCC, so skip it. See:
-  # http://lists.apple.com/archives/xcode-users/2011/Oct/msg00241.html
-  # https://github.com/mxcl/homebrew/pull/10550
-  def patches
-    DATA
-  end
-
   def install
     system "./configure", "--disable-dependency-tracking",
                           "--prefix=#{prefix}"
@@ -32,19 +26,3 @@ class Abyss < Formula
     system "#{bin}/ABYSS --version"
   end
 end
-
-__END__
-diff --git a/Map/Makefile.in b/Map/Makefile.in
-index 7a4e5a8..4dd5dd5 100644
---- a/Map/Makefile.in
-+++ b/Map/Makefile.in
-@@ -32,8 +32,7 @@ POST_INSTALL = :
- NORMAL_UNINSTALL = :
- PRE_UNINSTALL = :
- POST_UNINSTALL = :
--bin_PROGRAMS = abyss-index$(EXEEXT) abyss-map$(EXEEXT) \
--	abyss-overlap$(EXEEXT)
-+bin_PROGRAMS = abyss-index$(EXEEXT) abyss-map$(EXEEXT)
- subdir = Map
- DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
- ACLOCAL_M4 = $(top_srcdir)/aclocal.m4