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_38.96.tar.gz"
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sha256 "18d9c89b02c0ab044b2795a65f6236b2262a494ed83d27e31750437b350ef080"
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license "BSD-3-Clause"
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bottle do
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sha256 cellar: :any, arm64_monterey: "e5a3978e72e21c64260be9abc1e774fe7483068f20f535cbe69e8d0fdf74bbf4"
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sha256 cellar: :any, arm64_big_sur: "80d0cf1cabeb3e5b7444cc502f648f7f8bb3ba6b76eadc81285cce1c5ba72ee5"
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sha256 cellar: :any, monterey: "91b55caad3e49851078265f659be617177392ef7077a525cae1e4643a9db7049"
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sha256 cellar: :any, big_sur: "44e8a7318c8d619ff0a7cd2295869f158761d28ca197bdb2a6accf5a0937821c"
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sha256 cellar: :any, catalina: "3e306d31f8562469dbdb987ee78fbd1de6394fddfa17ded572dab05672cccdc9"
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sha256 cellar: :any_skip_relocation, x86_64_linux: "d02ef815958ec2fc729be2da6b814df18138de9a19b2ab237cf415bdad2de98a"
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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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