67 lines
2.7 KiB
Ruby
67 lines
2.7 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/2.3.4/abyss-2.3.4.tar.gz"
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sha256 "7bbe479d2574a4d0241a5f564852d637690ded165c160862977e90597c614fed"
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license all_of: ["GPL-3.0-only", "LGPL-2.1-or-later", "MIT", "BSD-3-Clause"]
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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: "ddaf94b4cc55d9eeba4af66371607f9b52d88f63199be9d8dca4b35a1e174409"
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sha256 cellar: :any, arm64_big_sur: "778a4b29c03b0e5a1157690e78a53ac4ed82dc881f59a42f416772be9194967e"
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sha256 cellar: :any, monterey: "c2e61ff154139048e0ffdd23dc2389344646a81ffbf7a211ec665d39cdb607f8"
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sha256 cellar: :any, big_sur: "ed5226b1b597566cbf966d7bf4cfc560027a5279ef444c1de2abad38ffaea5c6"
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sha256 cellar: :any, catalina: "d50e051d08efd49321441dbcccd8973505d9f5e75a5b5a126946ca41e5f2a673"
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sha256 cellar: :any_skip_relocation, x86_64_linux: "90f95159abd04629455507380bb7fd86ece2e658b1009b3c4dbd48fe0f934f2a"
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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("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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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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