62 lines
2.1 KiB
Ruby
62 lines
2.1 KiB
Ruby
class Mmseqs2 < Formula
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desc "Software suite for very fast sequence search and clustering"
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homepage "https://mmseqs.com/"
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url "https://github.com/soedinglab/MMseqs2/archive/11-e1a1c.tar.gz"
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version "11-e1a1c"
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sha256 "ffe1ae300dbe1a0e3d72fc9e947356a4807f07951cb56316f36974d8d5875cbb"
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license "GPL-3.0"
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revision 1
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head "https://github.com/soedinglab/MMseqs2.git"
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bottle do
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cellar :any_skip_relocation
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sha256 "9bc41128722a0a926cc30fca2cfb29574bb150deb8acc482cd61e7e49e8169fb" => :catalina
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sha256 "789fa0f2f9bef66df73de586236dbffb037f8a32794e47768818d1fc732c05e2" => :mojave
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sha256 "d3f8b1a3ba35b0af1e80a0a917d915e8c19ea542bde20879c3031f1138af55aa" => :high_sierra
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end
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depends_on "cmake" => :build
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depends_on "libomp"
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depends_on "wget"
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uses_from_macos "bzip2"
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uses_from_macos "zlib"
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resource "documentation" do
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url "https://github.com/soedinglab/MMseqs2.wiki.git",
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revision: "c77918c9cebb24075f3c102a73fb1d413017a1a5"
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end
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def install
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args = *std_cmake_args << "-DHAVE_TESTS=0" << "-DHAVE_MPI=0"
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args << "-DVERSION_OVERRIDE=#{version}"
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args << "-DHAVE_SSE4_1=1"
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libomp = Formula["libomp"]
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args << "-DOpenMP_C_FLAGS=-Xpreprocessor\ -fopenmp\ -I#{libomp.opt_include}"
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args << "-DOpenMP_C_LIB_NAMES=omp"
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args << "-DOpenMP_CXX_FLAGS=-Xpreprocessor\ -fopenmp\ -I#{libomp.opt_include}"
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args << "-DOpenMP_CXX_LIB_NAMES=omp"
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args << "-DOpenMP_omp_LIBRARY=#{libomp.opt_lib}/libomp.a"
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system "cmake", ".", *args
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system "make", "install"
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resource("documentation").stage { doc.install Dir["*"] }
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pkgshare.install "examples"
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bash_completion.install "util/bash-completion.sh" => "mmseqs.sh"
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end
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def caveats
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"MMseqs2 requires at least SSE4.1 CPU instruction support." unless Hardware::CPU.sse4?
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end
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test do
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system "#{bin}/mmseqs", "createdb", "#{pkgshare}/examples/QUERY.fasta", "q"
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system "#{bin}/mmseqs", "cluster", "q", "res", "tmp", "-s", "1"
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system "#{bin}/mmseqs", "createtsv", "q", "q", "res", "res.tsv"
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assert_predicate testpath/"res.tsv", :exist?
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assert_predicate (testpath/"res.tsv").size, :positive?
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end
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end
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