68 lines
2.8 KiB
Ruby
68 lines
2.8 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/software/abyss"
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url "https://github.com/bcgsc/abyss/releases/download/2.3.5/abyss-2.3.5.tar.gz"
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sha256 "5455f7708531681ee15ec4fd5620526a53c86d28f959e630dc495f526b7d40f7"
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license all_of: ["GPL-3.0-only", "LGPL-2.1-or-later", "MIT", "BSD-3-Clause"]
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revision 1
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livecheck do
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url :stable
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regex(/^v?(\d+(?:\.\d+)+)$/i)
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end
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bottle do
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sha256 cellar: :any, arm64_monterey: "4109a98fd3b68157787105d2d3da974641e5dc2fd6e63351c54e50a08305e199"
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sha256 cellar: :any, arm64_big_sur: "e294340bf5c2c91945d555a21215031cbefcba168645c80fb97ad83f334ac07d"
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sha256 cellar: :any, monterey: "ffca3c29f740aaa7ec67e51fc0f128d9feed8f016543b89cf1cb8c9f0aa60325"
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sha256 cellar: :any, big_sur: "8ae5a988cf8c7a5a9834d2a3db1613ae152bf6990ee6eae14a17bbe559baf129"
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sha256 cellar: :any, catalina: "7b591b8908cd7fa7dd97e26333457b20c0c60dcd32535cc07d39723014af3f90"
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sha256 cellar: :any_skip_relocation, x86_64_linux: "79df263bc4e91030e73f64d0348bbb7753d3ad190d5e30a562cbcc414b17d495"
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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 gcc: "5"
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fails_with :clang # no OpenMP support
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resource "homebrew-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("homebrew-testdata")
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if which("column")
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system "#{bin}/abyss-pe", "B=2G", "k=25", "name=ts", "in=reads1.fastq reads2.fastq"
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else
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# Fix error: abyss-tabtomd: column: not found
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system "#{bin}/abyss-pe", "B=2G", "unitigs", "scaffolds", "k=25", "name=ts", "in=reads1.fastq reads2.fastq"
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end
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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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