53 lines
1.9 KiB
Ruby
53 lines
1.9 KiB
Ruby
class Abyss < Formula
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desc "Genome sequence assembler for short reads"
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homepage "https://www.bcgsc.ca/resources/gsc-software-centre"
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url "https://github.com/bcgsc/abyss/releases/download/2.2.3/abyss-2.2.3.tar.gz"
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sha256 "ac7679ececbdd89cc050998eae31fa5f8bf7cdab6a0c05eb5eb1e3867c7e75cb"
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bottle do
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cellar :any
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sha256 "fe5e65727d390f31e0e847e30da9a6b931c7b1b5f3c0a4e6459b5aa0f4eb0ad9" => :catalina
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sha256 "d982f22bbc71a21271eb01441f4189366e91bfb3dc8c9718df09307eb89bf11e" => :mojave
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sha256 "482a9754933a932ca3d8860de7f753b72a1a344ddaf40104849ba999218d86a8" => :high_sierra
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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 "https://www.bcgsc.ca/sites/default/files/bioinformatics/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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ENV.delete("HOMEBREW_SDKROOT") if MacOS.version >= :mojave && MacOS::CLT.installed?
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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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