91 lines
3.7 KiB
Ruby
91 lines
3.7 KiB
Ruby
class Augustus < Formula
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desc "Predict genes in eukaryotic genomic sequences"
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homepage "https://bioinf.uni-greifswald.de/augustus/"
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url "https://github.com/Gaius-Augustus/Augustus/releases/download/v3.3.3/augustus-3.3.3.tar.gz"
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sha256 "4cc4d32074b18a8b7f853ebaa7c9bef80083b38277f8afb4d33c755be66b7140"
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license "Artistic-1.0"
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revision 2
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head "https://github.com/Gaius-Augustus/Augustus.git", branch: "master"
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livecheck do
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url "https://bioinf.uni-greifswald.de/augustus/binaries/"
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regex(/href=.*?augustus[._-]v?(\d+(?:\.\d+)+)\.t/i)
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end
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bottle do
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sha256 cellar: :any, arm64_monterey: "48d4e709de88d93f6c00b751cd2b70238eeed73c748267973aea6ef0a50a76c6"
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sha256 arm64_big_sur: "cf98b0583590e5c5c83bcae8357d9a510c18240b33b12c9f95ca4ec0318d61f4"
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sha256 cellar: :any, monterey: "d5346659a287d591d36110f987ae3becb64ab8d63cb940aaea46d68439208be4"
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sha256 cellar: :any, big_sur: "0ceda121d6ead1c2b3812f7e1a9155366751da603fd1ab6c0ccbcada6eebb668"
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sha256 cellar: :any, catalina: "526462eb67bf51a1b95fdecf402d67df75c876333adfabe5aedffe89d76946fc"
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sha256 cellar: :any, mojave: "1eab0e15ac3027334f0ccda5e4edce2d99cafeffcea50f486842aada76bf6212"
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sha256 cellar: :any_skip_relocation, x86_64_linux: "8271784fc43729dd82e83e031ef63bb278771c6ba271ff7c7bc17908abc56646"
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end
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# Fails to build with GCC 12
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# https://github.com/Homebrew/homebrew-core/pull/106755
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# https://github.com/Homebrew/homebrew-core/pull/40220
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deprecate! date: "2022-08-03", because: :does_not_build
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depends_on "boost" => :build
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depends_on "bamtools"
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uses_from_macos "zlib"
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on_macos do
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depends_on "gcc"
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end
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def install
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# Avoid "fatal error: 'sam.h' file not found" by not building bam2wig
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inreplace "auxprogs/Makefile", "cd bam2wig; make;", "#cd bam2wig; make;"
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# Fix error: api/BamReader.h: No such file or directory
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inreplace "auxprogs/bam2hints/Makefile",
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"INCLUDES = /usr/include/bamtools",
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"INCLUDES = #{Formula["bamtools"].include/"bamtools"}"
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inreplace "auxprogs/filterBam/src/Makefile",
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"BAMTOOLS = /usr/include/bamtools",
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"BAMTOOLS= #{Formula["bamtools"].include/"bamtools"}"
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# Prevent symlinking into /usr/local/bin/
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inreplace "Makefile", %r{ln -sf.*/usr/local/bin/}, "#ln -sf"
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# Compile executables for macOS. Tarball ships with executables for Linux.
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system "make", "clean"
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cd "src" do
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if OS.mac?
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# Clang breaks proteinprofile on macOS. This issue has been first reported
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# to upstream in 2016 (see https://github.com/nextgenusfs/funannotate/issues/3).
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# See also https://github.com/Gaius-Augustus/Augustus/issues/64
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gcc_major_ver = Formula["gcc"].any_installed_version.major
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with_env("HOMEBREW_CC" => Formula["gcc"].opt_bin/"gcc-#{gcc_major_ver}") do
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system "make"
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end
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else
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system "make"
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end
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end
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system "make"
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system "make", "install", "INSTALLDIR=#{prefix}"
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bin.env_script_all_files libexec/"bin", AUGUSTUS_CONFIG_PATH: prefix/"config"
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pkgshare.install "examples"
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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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AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
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EOS
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cmd = "#{bin}/augustus --species=human test.fasta"
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assert_match "Predicted genes", shell_output(cmd)
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cp pkgshare/"examples/example.fa", testpath
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cp pkgshare/"examples/profile/HsDHC.prfl", testpath
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cmd = "#{bin}/augustus --species=human --proteinprofile=HsDHC.prfl example.fa 2> /dev/null"
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assert_match "HS04636 AUGUSTUS gene 966 6903 1 + . g1", shell_output(cmd)
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end
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end
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