class Abyss < Formula desc "Genome sequence assembler for short reads" homepage "http://www.bcgsc.ca/platform/bioinfo/software/abyss" url "https://github.com/bcgsc/abyss/releases/download/2.1.5/abyss-2.1.5.tar.gz" sha256 "65bfc8241e6ff5adf7601ae4ae93a75e3db86d6bff5d593c75aaff7f0ef41757" revision 1 bottle do cellar :any sha256 "b3b0b70dd3911e0a94689f1ff4c0066a77f1698d6644e948a70b6cc073d2bcae" => :mojave sha256 "465013b8098487135b82083d9a73562d27dd856a1a9707d9a7946032e9828e02" => :high_sierra sha256 "7202018eb50f51b0fc6c5ae76339e7dd2ae712f4a2dcc71e8dff9eb812878b54" => :sierra end head do url "https://github.com/bcgsc/abyss.git" depends_on "autoconf" => :build depends_on "automake" => :build depends_on "multimarkdown" => :build end depends_on "boost" => :build depends_on "google-sparsehash" => :build depends_on "gcc" depends_on "open-mpi" fails_with :clang # no OpenMP support resource("testdata") do url "http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz" sha256 "28f8592203daf2d7c3b90887f9344ea54fda39451464a306ef0226224e5f4f0e" end def install system "./autogen.sh" if build.head? system "./configure", "--enable-maxk=128", "--prefix=#{prefix}", "--with-boost=#{Formula["boost"].include}", "--with-mpi=#{Formula["open-mpi"].prefix}", "--with-sparsehash=#{Formula["google-sparsehash"].prefix}", "--disable-dependency-tracking", "--disable-silent-rules" system "make", "install" end test do testpath.install resource("testdata") system "#{bin}/abyss-pe", "k=25", "name=ts", "in=reads1.fastq reads2.fastq" system "#{bin}/abyss-fac", "ts-unitigs.fa" end end