60 lines
2.8 KiB
Ruby
60 lines
2.8 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/archive/refs/tags/v3.5.0.tar.gz"
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sha256 "5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686"
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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", branch: "master"
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bottle do
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sha256 cellar: :any, arm64_ventura: "f1532d78fc1a8b788cf0f3bff293f0ca037157ea1bd84718e61063e6ceff1c4d"
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sha256 cellar: :any, arm64_monterey: "bb001f41a131cf3065eca32fe225afa567728d35b163f98dfd71a57b2aaf2a3d"
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sha256 cellar: :any, arm64_big_sur: "ce56e04aa4c4f706485616f2a7947ae59538391ec58100e20cbf5216bd3311a9"
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sha256 cellar: :any, ventura: "9e99bdba9516428b987face683ba441d663ede6ba43d00de363d2b21a24210f2"
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sha256 cellar: :any, monterey: "ae8d067cd836352d3aea30d22563eba8167fbc8223e24edfab93af36f623f63d"
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sha256 cellar: :any, big_sur: "955b4dc7f98c97aef46a05c8c1075054186bffa7b79bc49305ae8086f494ec02"
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sha256 cellar: :any, catalina: "0c01281063e3b4a3de714959e04e30229713e6043ea12fb050e546f7f69f62a8"
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sha256 cellar: :any_skip_relocation, x86_64_linux: "b9850f064f781034382d8f821bfffbb2d11492ead09af7f55ebe74a8756ccf8c"
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end
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depends_on "bamtools"
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depends_on "boost"
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depends_on "htslib"
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uses_from_macos "python" => :build, since: :catalina
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uses_from_macos "zlib"
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def install
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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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system "make", "COMPGENEPRED=false",
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"INCLUDE_PATH_BAMTOOLS=-I#{Formula["bamtools"].opt_include}/bamtools",
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"LIBRARY_PATH_BAMTOOLS=-L#{Formula["bamtools"].opt_lib}",
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"INCLUDE_PATH_HTSLIB=-I#{Formula["htslib"].opt_include}/htslib",
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"LIBRARY_PATH_HTSLIB=-L#{Formula["htslib"].opt_lib}"
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# Set PREFIX to prevent symlinking into /usr/local/bin/
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(buildpath/"tmp/bin").mkpath
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system "make", "install", "INSTALLDIR=#{prefix}", "PREFIX=#{buildpath}/tmp"
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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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