homebrew-core/Formula/augustus.rb

68 lines
2.6 KiB
Ruby

class Augustus < Formula
desc "Predict genes in eukaryotic genomic sequences"
homepage "https://bioinf.uni-greifswald.de/augustus/"
url "https://github.com/Gaius-Augustus/Augustus/releases/download/v3.3.3/augustus-3.3.3.tar.gz"
sha256 "4cc4d32074b18a8b7f853ebaa7c9bef80083b38277f8afb4d33c755be66b7140"
license "Artistic-1.0"
revision 1
head "https://github.com/Gaius-Augustus/Augustus.git"
bottle do
cellar :any
sha256 "9e6fc1d57f48cf314fa418059a9d619a8451d7e65ed8234225e52f311673cf6d" => :catalina
sha256 "476eeca3de3f98c4e539cee89078a3f37f667ae7f47ef375115439154bc23e3c" => :mojave
sha256 "b5077e94d1ee68864ed0d89bfc892ad80dcd37b89e149b23733bd9280d54771b" => :high_sierra
end
depends_on "boost" => :build
depends_on "bamtools"
depends_on "gcc"
def install
# Avoid "fatal error: 'sam.h' file not found" by not building bam2wig
inreplace "auxprogs/Makefile", "cd bam2wig; make;", "#cd bam2wig; make;"
# Fix error: api/BamReader.h: No such file or directory
inreplace "auxprogs/bam2hints/Makefile",
"INCLUDES = /usr/include/bamtools",
"INCLUDES = #{Formula["bamtools"].include/"bamtools"}"
inreplace "auxprogs/filterBam/src/Makefile",
"BAMTOOLS = /usr/include/bamtools",
"BAMTOOLS= #{Formula["bamtools"].include/"bamtools"}"
# Prevent symlinking into /usr/local/bin/
inreplace "Makefile", %r{ln -sf.*/usr/local/bin/}, "#ln -sf"
# Compile executables for macOS. Tarball ships with executables for Linux.
system "make", "clean"
# Clang breaks proteinprofile on macOS. This issue has been first reported
# to upstream in 2016 (see https://github.com/nextgenusfs/funannotate/issues/3).
# See also https://github.com/Gaius-Augustus/Augustus/issues/64
cd "src" do
with_env("HOMEBREW_CC" => Formula["gcc"].opt_bin/"gcc-#{Formula["gcc"].version_suffix}") do
system "make"
end
end
system "make"
system "make", "install", "INSTALLDIR=#{prefix}"
bin.env_script_all_files libexec/"bin", AUGUSTUS_CONFIG_PATH: prefix/"config"
pkgshare.install "examples"
end
test do
(testpath/"test.fasta").write <<~EOS
>U00096.2:1-70
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
EOS
cmd = "#{bin}/augustus --species=human test.fasta"
assert_match "Predicted genes", shell_output(cmd)
cp pkgshare/"examples/example.fa", testpath
cp pkgshare/"examples/profile/HsDHC.prfl", testpath
cmd = "#{bin}/augustus --species=human --proteinprofile=HsDHC.prfl example.fa 2> /dev/null"
assert_match "HS04636 AUGUSTUS gene 966 6903 1 + . g1", shell_output(cmd)
end
end