51 lines
1.9 KiB
Ruby
51 lines
1.9 KiB
Ruby
class Abyss < Formula
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desc "Genome sequence assembler for short reads"
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homepage "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
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url "https://github.com/bcgsc/abyss/releases/download/2.1.1/abyss-2.1.1.tar.gz"
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sha256 "aca9e5ad984282ced81038dfc20205ba0bb59ff4edf427419451b632aa567e9f"
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bottle do
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sha256 "80ab108b5ce547a63be711284367e2a29c7657eeee4f23ac0da1ec621113fe5f" => :mojave
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sha256 "47829fcb41eca26386d6c5db4b2d3d7ff999205ddea5db86059911cbd426fa3f" => :high_sierra
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sha256 "48729e38eecf5f49df1f05654a80e0539f5b44732f6ec43856e68b108dd96bce" => :sierra
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sha256 "e82ef97ceb8f9e93afd70c435fbf5798b15a96d7dd9c86e6cd79713c0064cc15" => :el_capitan
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end
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head do
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url "https://github.com/bcgsc/abyss.git"
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depends_on "autoconf" => :build
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depends_on "automake" => :build
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depends_on "multimarkdown" => :build
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end
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depends_on "boost" => :build
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depends_on "google-sparsehash" => :build
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depends_on "gcc"
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depends_on "open-mpi"
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fails_with :clang # no OpenMP support
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resource("testdata") do
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url "http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz"
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sha256 "28f8592203daf2d7c3b90887f9344ea54fda39451464a306ef0226224e5f4f0e"
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end
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def install
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system "./autogen.sh" if build.head?
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system "./configure", "--enable-maxk=128",
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"--prefix=#{prefix}",
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"--with-boost=#{Formula["boost"].include}",
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"--with-mpi=#{Formula["open-mpi"].prefix}",
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"--with-sparsehash=#{Formula["google-sparsehash"].prefix}",
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"--disable-dependency-tracking",
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"--disable-silent-rules"
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system "make", "install"
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end
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test do
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testpath.install resource("testdata")
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system "#{bin}/abyss-pe", "k=25", "name=ts", "in=reads1.fastq reads2.fastq"
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system "#{bin}/abyss-fac", "ts-unitigs.fa"
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end
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end
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