37 lines
1.0 KiB
Ruby
37 lines
1.0 KiB
Ruby
class PicardTools < Formula
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desc "Tools for manipulating HTS data and formats"
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homepage "https://broadinstitute.github.io/picard/"
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url "https://github.com/broadinstitute/picard/releases/download/2.25.5/picard.jar"
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sha256 "f7fa9784b84d384abfcbd77076f5ceab7b2797dc863ac35fd41470daa3efe3a5"
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license "MIT"
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livecheck do
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url :stable
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strategy :github_latest
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end
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bottle do
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sha256 cellar: :any_skip_relocation, all: "bdaf5ca6f12440de58e1513ae29215c776978e33b4093c27daa346d18258068b"
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end
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depends_on "openjdk"
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def install
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libexec.install "picard.jar"
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(bin/"picard").write <<~EOS
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#!/bin/bash
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exec "#{Formula["openjdk"].opt_bin}/java" $JAVA_OPTS -jar "#{libexec}/picard.jar" "$@"
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EOS
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end
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test do
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(testpath/"test.fasta").write <<~EOS
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>U00096.2:1-70
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AGCTTTTCATTCTGACTGCAACGGGCAATATGTCT
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CTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
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EOS
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cmd = "#{bin}/picard NormalizeFasta I=test.fasta O=/dev/stdout"
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assert_match "TCTCTG", shell_output(cmd)
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end
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end
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