47 lines
1.8 KiB
Ruby
47 lines
1.8 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-3.3.1.tar.gz"
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sha256 "e0249bff0345f6a790b5c56432f292040254457da22f1a2c212f42d7d2104087"
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bottle do
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sha256 "8ddcf0271ba6204c052ee9cb0d7e71fc68a2e5351e1b3dd6f09e74d6962fa1c3" => :high_sierra
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sha256 "79f8c3a53d545cd2be18e2581e8d66bb83f3643a2eb4a62553f24000c4c50f81" => :sierra
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sha256 "b8fd08dcad3d8a29d2615076a6a3603cfcec6526524db18269df7c62a8925e8e" => :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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# 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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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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