44 lines
1.5 KiB
Ruby
44 lines
1.5 KiB
Ruby
class Kallisto < Formula
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desc "Quantify abundances of transcripts from RNA-Seq data"
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homepage "https://pachterlab.github.io/kallisto/"
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url "https://github.com/pachterlab/kallisto/archive/v0.46.1.tar.gz"
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sha256 "492ef081395e8858fcd9832aceb8b61c79358f00afb45e6709146c0fb51dd231"
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bottle do
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cellar :any
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sha256 "4c690ce6fff7b1fe564feffde0f2804eead80692a10af99ae568c880d0e7b748" => :catalina
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sha256 "5ef9fc208160c101e37c01b74216ec48c9d6d53d16dffee4e434d4db36e378da" => :mojave
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sha256 "199940d786f8092d549b3b66379a289966c37f51719c076d5c387dadbaeb1f81" => :high_sierra
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end
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depends_on "autoconf" => :build
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depends_on "automake" => :build
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depends_on "cmake" => :build
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depends_on "hdf5"
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def install
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# Upstream issue 15 Feb 2018 "cmake does not run autoreconf for htslib"
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# https://github.com/pachterlab/kallisto/issues/159
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system "autoreconf", "-fiv", "ext/htslib"
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system "cmake", ".", *std_cmake_args
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# Upstream issue 15 Feb 2018 "parallelized build failure"
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# https://github.com/pachterlab/kallisto/issues/160
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# Upstream issue 15 Feb 2018 "cannot use system htslib"
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# https://github.com/pachterlab/kallisto/issues/161
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system "make", "htslib"
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system "make", "install"
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end
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test do
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(testpath/"test.fasta").write <<~EOS
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>seq0
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FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
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EOS
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output = shell_output("#{bin}/kallisto index -i test.index test.fasta 2>&1")
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assert_match "has 1 contigs and contains 32 k-mers", output
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end
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end
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