68 lines
2.4 KiB
Ruby
68 lines
2.4 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/2.3.1/abyss-2.3.1.tar.gz"
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sha256 "664045e7903e9732411effc38edb9ebb1a0c1b7636c64b3a14a681f465f43677"
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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 arm64_big_sur: "21d1cb2d31fa162cefea32db0630fc6011f8d3d0bb7ababa31f8e772820d1c7f"
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sha256 cellar: :any, big_sur: "e56ce6b9bf533fb34bd2f87e87fb1019e3cccdcdc94d0e665e144121c95ddcad"
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sha256 cellar: :any, catalina: "5a95037e8675013c34f4119d5a2914706ec3b99f522426878a19f27031ad4d79"
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sha256 cellar: :any, mojave: "fc1208b6ff7dbcdc23d621076a271a40f1090cab41690ce35433c81425984494"
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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 "open-mpi"
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on_macos do
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depends_on "gcc"
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end
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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", "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", "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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