56 lines
2.1 KiB
Ruby
56 lines
2.1 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/2.1.4/abyss-2.1.4.tar.gz"
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sha256 "2145a1727556104d6a14db06a9c06f47b96c31cc5ac595ae9c92224349bdbcfc"
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bottle do
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sha256 "8e6ea5b61adf547f7fe371892bda3d3cb8d09b5a659d75cc415b7734b7e18901" => :mojave
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sha256 "669b55b3d4b8ec60101bd17a3288a6afe54d558fc9c45cd0a73cd75e55f027aa" => :high_sierra
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sha256 "d6a05334fffcf0d456251082b294a15583a43031a02ec3ad4942de3006786c46" => :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 "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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# Fix a compiler error. Remove with the next release of abyss.
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# See https://github.com/bcgsc/abyss/commit/195f19bba03fec18d86cd931b34275222ba667fc
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inreplace "lib/bloomfilter/BloomFilter.hpp",
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'strncpy(header.magic, "BlOOMFXX", 8);',
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'memcpy(header.magic, "BlOOMFXX", 8);'
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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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