49 lines
2.2 KiB
Ruby
49 lines
2.2 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/v0.48.0.tar.gz"
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sha256 "1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0"
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license "BSD-2-Clause"
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bottle do
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sha256 cellar: :any_skip_relocation, arm64_ventura: "a77f40e079be6c8a6e762ae3c72cee556704605ef948b0a5b84278267a091fc2"
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sha256 cellar: :any_skip_relocation, arm64_monterey: "744b380617797b2d8e7de96fde867fde93d4a99e3be50e0ee55b4bfd63a6ead1"
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sha256 cellar: :any_skip_relocation, arm64_big_sur: "189fba3400b85552f7caa05058b92a8efe8115e89a488f92e5466982f6a03ca4"
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sha256 cellar: :any_skip_relocation, ventura: "8ba268ecbe91927be13f4b882a204132d77747ca2e9dc381cd84cb6b6b516342"
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sha256 cellar: :any_skip_relocation, monterey: "a3e87554317235569004690fb34c87590800f5e6159042dc587b454a39e43db9"
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sha256 cellar: :any_skip_relocation, big_sur: "ffc3507403994dfd317a6f63118879427239ee9a94c37bb4823f8a48ec9f8da2"
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sha256 cellar: :any_skip_relocation, catalina: "267cdea1b28358181c8701dd4bf0d2ed297df3be0298c80499199f89aa6bd6de"
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sha256 cellar: :any_skip_relocation, x86_64_linux: "20207d99e10ff85645eb4b3ceec5359e74af6772bc51496a48c00807d4a9eabe"
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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 "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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