45 lines
1.6 KiB
Ruby
45 lines
1.6 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/v0.44.0.tar.gz"
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sha256 "35a81201a56f4557697e6fe693dc6b701bbbd0a7b2b6e1c6c845ef816d67ca29"
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revision 1
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bottle do
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cellar :any
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sha256 "2b4aa9e98aaa90703a678a425e1986a05ef2aad15a6ae5e1809fee4d99c6a909" => :mojave
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sha256 "ab38b73fea94b87a8bb4a177a0c8d521bf91d5cd5476cd5b0237f2ea007ebefd" => :high_sierra
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sha256 "aae08244ae475a38fe28b7d33b1ce48880f48e3905451e813ba88c9bf69eda77" => :sierra
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sha256 "de0c2d1d3ec0b36aae9a536e890dab249bba372f26d6e72dc70d39e5ea3d29e9" => :el_capitan
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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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