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beast.rb
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beast.rb
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class Beast < Formula
desc "Bayesian Evolutionary Analysis Sampling Trees"
homepage "http://beast.bio.ed.ac.uk/"
# doi "10.1093/molbev/mss075"
# tag "bioinformatics"
url "https://github.com/beast-dev/beast-mcmc/archive/v1.8.3.tar.gz"
sha256 "1b03318e77064f8d556a0859aadd3c81036b41e56e323364fb278a56a00aff44"
head "https://github.com/beast-dev/beast-mcmc.git"
bottle do
cellar :any_skip_relocation
sha256 "82fa3516a312aaee005f9dbc92999a2d2eeef1ba1b50eac35e0f889a1bc76dce" => :el_capitan
sha256 "52c9e1b8d502d97239fa94b86e3a64ad91fdcb741513710b3fb85b6dc405e2a1" => :yosemite
sha256 "10340f6d4d33d941f5c0064933919d5072064120a434eb5d8fa1c29cde194f7f" => :mavericks
sha256 "55d3f39de9fe6938a7f203ad8302de011a3271ee2c273e3c85c4bf0b423964c7" => :x86_64_linux
end
depends_on :ant => :build
def install
system "ant", "linux"
prefix.install Dir["release/Linux/BEASTv*/*"]
# Move installed JARs to libexec
mv lib, libexec
# Point wrapper scripts to libexec
inreplace Dir[bin/"*"] do |s|
s["$BEAST/lib"] = "$BEAST/libexec"
end
end
def caveats; <<-EOS.undent
Examples are installed in:
#{opt_prefix}/examples/
EOS
end
test do
cp (opt_prefix/"examples"/"clockModels"/"testUCRelaxedClockLogNormal.xml"), testpath
# Run fewer generations to speed up tests
inreplace "testUCRelaxedClockLogNormal.xml" do |s|
s['chainLength="10000000"'] = 'chainLength="500000"'
end
system "#{bin}/beast", "-beagle_off", "testUCRelaxedClockLogNormal.xml"
%W[ops log trees].each do |ext|
assert File.exist? "testUCRelaxedClockLogNormal." + ext
end
end
end