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/v0.46.2.tar.gz"
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sha256 "c447ca8ddc40fcbd7d877d7c868bc8b72807aa8823a8a8d659e19bdd515baaf2"
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license "BSD-2-Clause"
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bottle do
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sha256 cellar: :any_skip_relocation, arm64_monterey: "d7b9aff623b0268cfdf089a7869dd01eec0d7f54ca1e2bb065567e26296093f8"
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sha256 cellar: :any_skip_relocation, arm64_big_sur: "51a7725f81265fe4530962417b874176e534f916cad432db1cb2d5c5840da3a6"
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sha256 cellar: :any_skip_relocation, monterey: "f400337f4259327b35a0c1e0d779e3488aa9b26ae4a6c4a3a4275b3946279ca3"
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sha256 cellar: :any_skip_relocation, big_sur: "2c004978635382869062996fed516c2edd83597d3e2221984759fc32955854e5"
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sha256 cellar: :any_skip_relocation, catalina: "7ef1f941663072b0a57597992acf8203ba3664129f305cb8626c0c346e51bf0c"
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sha256 cellar: :any_skip_relocation, mojave: "b2e59c1cc0fc1b07d02bab1cbc1533bcca1edf4bc0b81791d5ac597a7b84cce0"
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sha256 cellar: :any_skip_relocation, high_sierra: "8491424ec8d4f8e170315e13c5f3bb92895b608c9c7108f260459e06bbbf73f9"
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sha256 cellar: :any_skip_relocation, x86_64_linux: "ca9d61869fb10b292f1ecc95329cb3905834e42a8d46cfc6b6bec177406b9b66"
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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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