48 lines
2.2 KiB
Ruby
48 lines
2.2 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_39.01.tar.gz"
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sha256 "98608da50130c47f3abd095b889cc87f60beeb8b96169b664bc9d849abe093e6"
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license "BSD-3-Clause"
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bottle do
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sha256 cellar: :any, arm64_ventura: "ee5b3030f1acfe5105146f15689f3593356eeb1fcd783304d82120a5799e53ca"
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sha256 cellar: :any, arm64_monterey: "4f724b3391445cb3801dd8add9f385111f5d0ce8df1fde3956b71c7778df1a31"
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sha256 cellar: :any, arm64_big_sur: "8f5328602a99242b650931945bd1ad3b3fbd4da8c8ebb76a615148835fcbeb27"
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sha256 cellar: :any, ventura: "1e020f4b8b859f2d173f42c86eb8d6f03c90f4b33c4881722d32f0375d7cb500"
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sha256 cellar: :any, monterey: "fa2231392ff7a5cc23c618d3ede17dabf7c39fcab96af981f34a44d255d56986"
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sha256 cellar: :any, big_sur: "91b2d7d2cda27ae13fd9aa955874f5a3be3af97b481ee5d23ac10e09c54da33f"
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sha256 cellar: :any, catalina: "2edf1f85161f3a245b29fb55b117f074d04c0859cc1abbb9406ac98c038c7730"
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sha256 cellar: :any_skip_relocation, x86_64_linux: "177acf4ad3c84029f0f067afc3c4838e8cc91ec4f693a02554eedcbd86a3f379"
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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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