45 lines
1.6 KiB
Ruby
45 lines
1.6 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.tar.gz"
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sha256 "b5eb811a4c33a2cc3bbd16355e19d530eeac6d1ac923e59f48d7a79f396234ee"
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revision 1
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bottle do
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sha256 "6ffeac4edd4805321ea0957959f85da8cc1f5978cdc8a98903a78c407d5d183e" => :high_sierra
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sha256 "b87f6e5824186aaa1a02cc6665dde1328a4255aed653de85edd3e4bd40f65c60" => :sierra
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sha256 "19a761ef4afa0cd5e9699b59b11eaac2e7e1d3dbfa14e2c8ced1b27eb57c2c1e" => :el_capitan
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end
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depends_on "bamtools"
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depends_on "boost"
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def install
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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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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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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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end
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end
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