66 lines
2.5 KiB
Ruby
66 lines
2.5 KiB
Ruby
class Augustus < Formula
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desc "Predict genes in eukaryotic genomic sequences"
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homepage "http://bioinf.uni-greifswald.de/augustus/"
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url "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.2.tar.gz"
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sha256 "989a95fe3a83d62af4d323a9727d11b2c566adcf4d789d5d86d7b842d83e7671"
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head "https://github.com/Gaius-Augustus/Augustus.git"
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bottle do
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cellar :any
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rebuild 1
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sha256 "4d052d58f6a1432deabdb529c83774017cc51456e780fd0dc79d127db2593366" => :mojave
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sha256 "54dfd9c7cb44e36d126ac9d1febe79192a5c9fa71e11b9e5bb9a3b6aa14ed3bf" => :high_sierra
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sha256 "a6fdc891239b33bea15d9f3f87992e5bf37a9b82ef683e662331617c1ac3c980" => :sierra
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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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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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with_env("HOMEBREW_CC" => "gcc-9") 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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