smalt 0.7.6: rebuild (#1837)

Formula/smalt.rb

@@ -1,23 +1,56 @@
 class Smalt < Formula
   desc "Aligns DNA sequencing reads with a reference genome"
-  homepage "https://www.sanger.ac.uk/science/tools/smalt-0"
+  homepage "https://sourceforge.net/projects/smalt/"
   url "https://downloads.sourceforge.net/project/smalt/smalt-0.7.6.tar.gz"
   sha256 "89ccdfe471edba3577b43de9ebfdaedb5cd6e26b02bf4000c554253433796b31"
-  license "GPL-3.0"
+  license "GPL-3.0-or-later"
 
   bottle do
     root_url "https://ghcr.io/v2/brewsci/bio"
     sha256 cellar: :any_skip_relocation, sierra:       "cd6b0f671a4a141122aab57c88d3d73164b0730391dfebb7f3e9e3696bb3a124"
     sha256 cellar: :any_skip_relocation, x86_64_linux: "80e68892a948076affec7e1157924798eb01ae4f15e78103eb2d809cb30aa92c"
   end
 
+  depends_on "autoconf" => :build
+  depends_on "automake" => :build
+  depends_on "gettext" => :build
+  depends_on "libtool" => :build
+  depends_on "pkg-config" => :build
+  depends_on "samtools"
+
+  uses_from_macos "zlib"
+
+  resource "bambamc" do
+    url "https://github.com/gt1/bambamc/archive/refs/tags/0.0.50-release-20140430085950.tar.gz"
+    sha256 "06d2f17b9e4290ef76275f5011dab3b9967baa4d960c2c42f315c7c2f8a89d04"
+  end
+
   resource "manual" do
     url "https://downloads.sourceforge.net/project/smalt/smalt_manual.pdf"
     sha256 "efd52e8429237b27797027477c33e1071f6247616d7705106af256e48307480a"
   end
 
   def install
-    system "./configure", "--prefix=#{prefix}"
+    resource("bambamc").stage do
+      system "autoreconf", "-fvi"
+      system "./configure", "--prefix=#{prefix}/bambamc"
+      system "make", "install"
+    end
+
+    # add ldflags to find the libbambamc
+    ldflags = "-Wl,-rpath -Wl,#{prefix}/bambamc/lib -L#{prefix}/bambamc/lib"
+    args = std_configure_args + %W[
+      --with-bambamc=yes
+      PKG_CONFIG_PATH=#{prefix}/bambamc/lib/pkgconfig
+      CFLAGS=-I#{prefix}/bambamc/include
+      LDFLAGS=#{ldflags}
+      LIBS=-lbambamc
+    ]
+    # No longer used -lbam in the latest samtools
+    inreplace "configure", "-lbam", ""
+    # Fix error: archive member 'libseq.a' not a mach-o file
+    inreplace ["src/Makefile.am", "src/Makefile.in"], "libsgm_a_LIBADD = libseq.a", "libsgm_a_LIBADD = "
+    system "./configure", *args
     system "make"
     system "make", "install"
     doc.install resource("manual")