77 lines
3.1 KiB
Ruby
77 lines
3.1 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 1
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head "https://github.com/Gaius-Augustus/Augustus.git"
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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_big_sur: "03665ee18df08813482e9ad6b91ff670ea332f828f6a0873ceef68dc0d574048"
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sha256 cellar: :any, big_sur: "95ce85b389842f3b394dad647c2917ca16609acfdbb6e9b1f949250ac7beb84a"
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sha256 cellar: :any, catalina: "9e6fc1d57f48cf314fa418059a9d619a8451d7e65ed8234225e52f311673cf6d"
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sha256 cellar: :any, mojave: "476eeca3de3f98c4e539cee89078a3f37f667ae7f47ef375115439154bc23e3c"
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sha256 cellar: :any, high_sierra: "b5077e94d1ee68864ed0d89bfc892ad80dcd37b89e149b23733bd9280d54771b"
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end
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depends_on "boost" => :build
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depends_on "bamtools"
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depends_on "gcc"
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uses_from_macos "zlib"
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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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# 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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cd "src" do
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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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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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