45 lines
2.2 KiB
Ruby
45 lines
2.2 KiB
Ruby
class Jellyfish < Formula
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desc "Fast, memory-efficient counting of DNA k-mers"
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homepage "http://www.genome.umd.edu/jellyfish.html"
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url "https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-2.3.0.tar.gz"
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sha256 "e195b7cf7ba42a90e5e112c0ed27894cd7ac864476dc5fb45ab169f5b930ea5a"
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license any_of: ["BSD-3-Clause", "GPL-3.0-or-later"]
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bottle do
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sha256 cellar: :any, arm64_ventura: "9e0526e92d9b87bb9c26732174f0aa7b700db587e965941bd79d1bfc761a8b3e"
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sha256 cellar: :any, arm64_monterey: "3368a53a61d961a9169a4156a60d8023aee069084c108d67e8b81d12c01e5106"
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sha256 cellar: :any, arm64_big_sur: "15ceae21239d0a1f851e878d20889ef5539b121222153829b3b1e2dcb6cc2548"
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sha256 cellar: :any, ventura: "d1331785c605eee45bfa7053ad06da959b624d2af91c5a032da5350b0c1820f2"
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sha256 cellar: :any, monterey: "00ffb57295d4f3362c58fc69bb017c183efbb7a7533a57d49cbf2dd83ca4d5cb"
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sha256 cellar: :any, big_sur: "04b22121bce09df2e3cee997d3973a12e9f58e9b5e928465502eb4e83d429352"
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sha256 cellar: :any, catalina: "0ce228d3b386be6f7e10bed1186abfc74544658e092defaa4a7001a06c7f0eed"
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sha256 cellar: :any, mojave: "78083728d3d3d1cba0ec71786d1f633c4a626c1b64432ce46f84dacfb0a714d6"
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sha256 cellar: :any_skip_relocation, x86_64_linux: "1e1922bf36c12b1d56d19e1ead6bd461000bd7ed19a8ac5cfd4398f2bbd54e61"
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end
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depends_on "autoconf@2.69" => :build
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depends_on "automake" => :build
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depends_on "gettext" => :build
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depends_on "libtool" => :build
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depends_on "pkg-config" => :build
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depends_on "htslib"
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def install
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# autoreconf to fix flat namespace detection bug.
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system "autoreconf", "-fvi"
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system "./configure", *std_configure_args
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system "make"
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system "make", "install"
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end
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test do
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(testpath/"test.fa").write <<~EOS
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>Homebrew
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AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
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EOS
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system "#{bin}/jellyfish", "count", "-m17", "-s100M", "-t2", "-C", "test.fa"
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assert_match "1 54", shell_output("#{bin}/jellyfish histo mer_counts.jf")
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assert_match(/Unique:\s+54/, shell_output("#{bin}/jellyfish stats mer_counts.jf"))
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end
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end
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