51 lines
2.5 KiB
Ruby
51 lines
2.5 KiB
Ruby
class Bioperl < Formula
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desc "Perl tools for bioinformatics, genomics and life science"
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homepage "https://bioperl.org"
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url "https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.7.8.tar.gz"
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sha256 "c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738"
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license any_of: ["Artistic-1.0-Perl", "GPL-1.0-or-later"]
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head "https://github.com/bioperl/bioperl-live.git", branch: "master"
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# We specifically match versions with three numeric parts because upstream
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# documentation mentions that release versions have three parts and there are
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# older tarballs with fewer than three parts that we need to omit for version
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# comparison to work correctly.
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livecheck do
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url :stable
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regex(/href=["']?BioPerl[._-]v?(\d+\.\d+\.\d+)(?:\.?_\d+)?\.t/i)
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end
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bottle do
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sha256 cellar: :any_skip_relocation, arm64_monterey: "eca523bdef4f935b8887b120307c4841372c1a349d96255cd173fb2bd4ade142"
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sha256 cellar: :any_skip_relocation, arm64_big_sur: "edad2306b7e911884abc787c59cb8ce91ae5cc59d4fad4373bade3a11fc3806a"
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sha256 cellar: :any_skip_relocation, monterey: "2e449a33bfdec93ad0429d62ad331d41f3aefc1e7add30daf584518f941fd9a5"
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sha256 cellar: :any_skip_relocation, big_sur: "c876cdb3cc4f70f3251d57fe47c3fbb6ec9a303df8dbaa276f0b8072ca39d1c9"
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sha256 cellar: :any_skip_relocation, catalina: "631f46b74bf805d23a414d34961f8e14fe2f0be2224522dfe3eb6f73a7adbb0d"
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sha256 cellar: :any_skip_relocation, mojave: "a284378a572edc991e964002c99b6991d4fb37610dfcd9f6abd8587b16962896"
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sha256 cellar: :any_skip_relocation, x86_64_linux: "6baaf72a4d61a3e466ecd8c02a2943e3408d880177df58a45279c16bfe72b2f2"
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end
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depends_on "cpanminus" => :build
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depends_on "pkg-config" => :build
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depends_on "perl"
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uses_from_macos "zlib"
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def install
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ENV.prepend_create_path "PERL5LIB", libexec/"lib/perl5"
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system "cpanm", "--self-contained", "-l", libexec, "DBI" unless OS.mac?
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system "cpanm", "--verbose", "--self-contained", "-l", libexec, "."
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bin.env_script_all_files libexec, "PERL5LIB" => ENV["PERL5LIB"]
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libexec.glob("bin/bp_*") do |executable|
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(bin/executable.basename).write_env_script executable, PERL5LIB: ENV["PERL5LIB"]
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end
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end
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test do
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(testpath/"test.fa").write ">homebrew\ncattaaatggaataacgcgaatgg"
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assert_match ">homebrew\nH*ME*REW", shell_output("#{bin}/bp_translate_seq < test.fa")
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assert_match(/>homebrew-100_percent-1\n[atg]/, shell_output("#{bin}/bp_mutate -i test.fa -p 100 -n 1"))
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assert_match "GC content is 0.3750", shell_output("#{bin}/bp_gccalc test.fa")
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end
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end
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