roary 3.13.0 (#1819)

Formula/roary.rb

@@ -0,0 +1,64 @@
+class Roary < Formula
+  # cite Page_2015: "https://doi.org/10.1093/bioinformatics/btv421"
+  desc "High speed stand alone pan-genome pipeline"
+  homepage "https://sanger-pathogens.github.io/Roary/"
+  url "https://github.com/sanger-pathogens/Roary/archive/refs/tags/v3.13.0.tar.gz"
+  sha256 "375f83c8750b0f4dea5b676471e73e94f3710bc3a327ec88b59f25eae1c3a1e8"
+  license "GPL-3.0-or-later"
+
+  bottle do
+    root_url "https://ghcr.io/v2/brewsci/bio"
+    sha256 cellar: :any, catalina:     "94907f6c61003dd602970c9c878fc7171bf2be0ddfee3d1db2ebd5a04869837a"
+    sha256 cellar: :any, x86_64_linux: "74f824cff0367696af1bafe8c74f61dc17f3115506734a6f5604e91d96e2d830"
+  end
+
+  depends_on "cpanminus" => :build
+  depends_on "bedtools"
+  depends_on "bioperl"
+  depends_on "blast"
+  depends_on "brewsci/bio/cd-hit"
+  depends_on "brewsci/bio/fasttree"
+  depends_on "brewsci/bio/kraken"
+  depends_on "brewsci/bio/mcl"
+  depends_on "brewsci/bio/prank"
+  depends_on "mafft"
+  depends_on "openssl@3"
+  depends_on "parallel"
+  depends_on "perl"
+
+  uses_from_macos "libxml2"
+
+  def install
+    libexec.install Dir["bin/*"]
+    pkgshare.install "contrib"
+
+    # let CPAN install these
+    rm_r buildpath/"lib"
+    rm_r buildpath/"t"
+    rm_r buildpath/"bin"
+    bin.mkpath
+
+    ENV.prepend "PERL5LIB", Formula["perl"].libexec/"lib/perl5"
+    ENV.prepend_create_path "PERL5LIB", prefix/"perl5/lib/perl5"
+
+    # --notest because https://github.com/sanger-pathogens/Roary/issues/386
+    system "cpanm", "--notest", "--self-contained", "-l", prefix/"perl5", "Bio::Roary"
+
+    Dir[libexec/"*"].each do |exe|
+      name = File.basename exe
+      (bin/name).write_env_script(exe, PERL5LIB: ENV["PERL5LIB"])
+    end
+  end
+
+  def caveats
+    <<~EOS
+      The included .R scripts need R and ggplot2 to be installed separately.
+    EOS
+  end
+
+  test do
+    assert_match version.to_s, shell_output("#{bin}/roary -w 2>&1")
+    assert_match version.to_s, shell_output("#{bin}/roary -a 2>&1")
+    assert_match "core", shell_output("#{bin}/roary -h 2>&1")
+  end
+end