meme@4 4.12.0 (#1678)

Formula/meme@4.rb

@@ -0,0 +1,58 @@
+class MemeAT4 < Formula
+  # cite Bailey_2009: "https://doi.org/10.1093/nar/gkp335"
+  desc "Tools for motif discovery"
+  homepage "https://meme-suite.org"
+  url "https://meme-suite.org/meme/meme-software/4.12.0/meme_4.12.0.tar.gz"
+  sha256 "49ff80f842b59d328588acfcd1d15bf94c55fed661d22b0f95f37430cc363a06"
+  license :cannot_represent
+
+  keg_only :versioned_formula
+
+  depends_on "ghostscript"
+  depends_on "open-mpi"
+  depends_on "python@3.12"
+
+  uses_from_macos "libxml2"
+  uses_from_macos "libxslt"
+  uses_from_macos "perl"
+  uses_from_macos "zlib"
+
+  resource "XML::Parser" do
+    url "https://cpan.metacpan.org/authors/id/T/TO/TODDR/XML-Parser-2.47.tar.gz"
+    sha256 "ad4aae643ec784f489b956abe952432871a622d4e2b5c619e8855accbfc4d1d8"
+  end
+
+  def install
+    ENV.append "CFLAGS", "-fcommon -fgnu89-inline"
+    ENV.append "LDFLAGS", "-Wl,--allow-multiple-definition" if OS.linux?
+    inreplace "src/mast.h", "#include <sys/types.h>\n", "#include <sys/types.h>\n#include <sys/wait.h>\n"
+
+    unless OS.mac?
+      ENV.prepend_create_path "PERL5LIB", libexec/"lib/perl5"
+      perl_resources = %w[XML::Parser]
+      perl_resources.each do |r|
+        resource(r).stage do
+          system "perl", "Makefile.PL", "INSTALL_BASE=#{libexec}"
+          system "make", "PERL5LIB=#{ENV["PERL5LIB"]}"
+          system "make", "install"
+        end
+      end
+    end
+
+    system "./configure",
+      "--disable-dependency-tracking",
+      "--prefix=#{prefix}",
+      "--with-mpidir=#{Formula["open-mpi"].opt_prefix}",
+      "--with-url=https://meme-suite.org/meme" \
+      "--with-python3=#{Formula["python@3.12"].opt_bin}/python3",
+      "--with-gs=#{Formula["ghostscript"].opt_bin}/gs"
+
+    system "make", "install"
+    bin.env_script_all_files libexec/"bin", PERL5LIB: ENV["PERL5LIB"] if OS.linux?
+    pkgshare.install "tests/common/At.s"
+  end
+
+  test do
+    system bin/"meme", pkgshare/"At.s"
+  end
+end