46 lines
2.0 KiB
Ruby
46 lines
2.0 KiB
Ruby
class Bbtools < Formula
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desc "Brian Bushnell's tools for manipulating reads"
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homepage "https://jgi.doe.gov/data-and-tools/bbtools/"
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url "https://downloads.sourceforge.net/bbmap/BBMap_38.97.tar.gz"
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sha256 "1bb0baf9e57e699982d7bd965942fe9f7462aba92e4fee3db19aeeb077a5aafe"
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license "BSD-3-Clause"
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bottle do
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sha256 cellar: :any, arm64_monterey: "4b8cc8fff665314729772d1ea64c307b784b9c4603622494f53a2f57e060f190"
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sha256 cellar: :any, arm64_big_sur: "ca46c105b647a8d7aae4c078584b98f8d1ea40a11699d7f7b7610fa360a5136f"
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sha256 cellar: :any, monterey: "78471c7b433f8cacb232a44d9fb0d3b02b949a71b65a53809309cc7b2f435b32"
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sha256 cellar: :any, big_sur: "f296c28ee9547aa584a89aeb870f84f31f343904800335501e7e343b17e10a07"
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sha256 cellar: :any, catalina: "c4b077b247c047eeb75b0b1d69bfb97f00c5a78a1e036a68efacd01991db943a"
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sha256 cellar: :any_skip_relocation, x86_64_linux: "8f531f6bd46cccc7971d04b99dfe2368c0c06a335d1135a97f296abab0e42dfb"
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end
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depends_on "openjdk"
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def install
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cd "jni" do
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rm Dir["libbbtoolsjni.*", "*.o"]
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system "make", "-f", OS.mac? ? "makefile.osx" : "makefile.linux"
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end
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libexec.install %w[current jni resources]
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libexec.install Dir["*.sh"]
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bin.install Dir[libexec/"*.sh"]
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bin.env_script_all_files(libexec, Language::Java.overridable_java_home_env)
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doc.install Dir["docs/*"]
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end
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test do
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res = libexec/"resources"
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args = %W[in=#{res}/sample1.fq.gz
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in2=#{res}/sample2.fq.gz
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out=R1.fastq.gz
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out2=R2.fastq.gz
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ref=#{res}/phix174_ill.ref.fa.gz
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k=31
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hdist=1]
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system "#{bin}/bbduk.sh", *args
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assert_match "bbushnell@lbl.gov", shell_output("#{bin}/bbmap.sh")
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assert_match "maqb", shell_output("#{bin}/bbmap.sh --help 2>&1")
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assert_match "minkmerhits", shell_output("#{bin}/bbduk.sh --help 2>&1")
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end
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end
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