freebayes 1.3.9

autobump: add freebayes

Signed-off-by: Rui Chen <[email protected]>

Author: chenrui333

.github/autobump.txt

@@ -1070,6 +1070,7 @@ fping
 fplll
 fq
 fred
+freebayes
 freeciv
 freeglut
 freeipmi

Formula/f/freebayes.rb

@@ -1,44 +1,13 @@
 class Freebayes < Formula
   desc "Bayesian haplotype-based genetic polymorphism discovery and genotyping"
   homepage "https://github.com/freebayes/freebayes"
+  # pull from git tag to get submodules
+  url "https://github.com/freebayes/freebayes.git",
+      tag:      "v1.3.9",
+      revision: "ab36d1f789c039ba872f5d911ce6ff09952dc329"
   license "MIT"
   head "https://github.com/freebayes/freebayes.git", branch: "master"
 
-  stable do
-    # Use tarball and resources as workaround for https://github.com/freebayes/freebayes/pull/799
-    url "https://github.com/freebayes/freebayes/archive/refs/tags/v1.3.8.tar.gz"
-    sha256 "d1c24b1d1b35277e7403cd67063557998218a105c916b01a745e7704715fce67"
-
-    depends_on "cmake" => :build
-    depends_on "pybind11" => :build
-    depends_on "simde" => :build
-
-    on_macos do
-      depends_on "libomp" => :build
-    end
-
-    resource "contrib/smithwaterman" do
-      url "https://github.com/ekg/smithwaterman/archive/2610e259611ae4cde8f03c72499d28f03f6d38a7.tar.gz"
-      sha256 "8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8"
-    end
-
-    resource "contrib/fastahack" do
-      url "https://github.com/ekg/fastahack/archive/bb332654766c2177d6ec07941fe43facf8483b1d.tar.gz"
-      sha256 "552a1b261ea90023de7048a27c53a425a1bc21c3fb172b3c8dc9f585f02f6c43"
-    end
-
-    resource "contrib/multichoose" do
-      url "https://github.com/vcflib/multichoose/archive/255192edd49cfe36557f7f4f0d2d6ee1c702ffbb.tar.gz"
-      sha256 "0045051ee85d36435582151830efe0eefb466be0ec9aedbbc4465dca30d22102"
-    end
-
-    resource "contrib/vcflib" do
-      url "https://github.com/vcflib/vcflib.git",
-          tag:      "v1.0.10",
-          revision: "2ad261860807e66dbd9bcb07fee1af47b9930d70"
-    end
-  end
-
   # The Git repository contains a few older tags that erroneously omit a
   # leading zero in the version (e.g., `v9.9.2` should have been `v0.9.9.2`)
   # and these would appear as the newest versions until the current version
@@ -58,40 +27,76 @@ class Freebayes < Formula
     sha256               x86_64_linux:  "056ef004633b4ad83902199054e990313f0e2654455ebe17f822b28d5a7add9a"
   end
 
+  depends_on "cmake" => :build # for vcflib
   depends_on "meson" => :build
   depends_on "ninja" => :build
   depends_on "pkgconf" => :build
+  depends_on "pybind11" => :build # for vcflib
+  depends_on "simde" => :build
+  depends_on "wfa2-lib" => :build # for vcflib
+  depends_on "xz" => :build # for vcflib
   depends_on "htslib"
-  depends_on "xz"
 
-  uses_from_macos "zlib"
+  uses_from_macos "bzip2" => :build # for vcflib
+  uses_from_macos "zlib" => :build # for vcflib
+
+  on_macos do
+    depends_on "libomp" => :build # for vcflib
+  end
+
+  resource "vcflib" do
+    url "https://github.com/vcflib/vcflib/releases/download/v1.0.12/vcflib-1.0.12-src.tar.gz"
+    sha256 "cb1e78d675f06ae3b22ffed7e1dea317e4c7f826e51e5b5dabd80240efbe1019"
+
+    # Backport fix for using external `wfa2-lib`
+    patch do
+      url "https://github.com/vcflib/vcflib/commit/5e4edec2fba5d5a51dae7a9fe48d0252ade53857.patch?full_index=1"
+      sha256 "e7d6d433d837dd823916ef91fe0165bf4ba4f05c52fd4c9517aef7f80653a2a8"
+    end
+
+    # Apply open PR to help find `wfa2-lib` include directory
+    # PR ref: https://github.com/vcflib/vcflib/pull/413
+    patch do
+      url "https://github.com/vcflib/vcflib/commit/9f9237ff0e6b4887f0edfc88587957aa736ced7b.patch?full_index=1"
+      sha256 "bede43d22b4b47141cd90edc4df90f65b9ac41e9598c2b05b2fe7fa84ea51aa8"
+    end
+  end
+
+  # Apply open PR to help Meson locate vcflib and wfa2 libraries
+  # PR ref: https://github.com/freebayes/freebayes/pull/822
+  patch do
+    url "https://github.com/freebayes/freebayes/commit/b458396e1acbad3983c70c202a6db2b3711a8eac.patch?full_index=1"
+    sha256 "b5c7d855d4d66c6c96dada307e82ccbf0b6904a25928c4f3e163f52e178b7907"
+  end
+
+  # Apply open PR to fix build when using git submodules
+  # PR ref: https://github.com/freebayes/freebayes/pull/823
+  patch do
+    url "https://github.com/freebayes/freebayes/commit/35eeacb6468fdce25233a33f7216f4e776d381f9.patch?full_index=1"
+    sha256 "1b6f0bb1e369a4b11e9a7754f3b789035b39cc5d9e3dbbac84fde21893f0d9be"
+  end
 
   def install
-    if build.stable?
-      resources.each { |r| (buildpath/r.name).install r }
+    resource("vcflib").stage do
+      rm_r(["contrib/WFA2-lib", "contrib/tabixpp/htslib"]) # avoid bundled libraries
 
-      system "cmake", "-S", "contrib/vcflib", "-B", "build_vcflib",
+      system "cmake", "-S", ".", "-B", "build",
                       "-DBUILD_DOC=OFF",
                       "-DBUILD_ONLY_LIB=ON",
                       "-DZIG=OFF",
                       *std_cmake_args(install_prefix: buildpath/"vendor")
-      system "cmake", "--build", "build_vcflib"
-      system "cmake", "--install", "build_vcflib"
+      system "cmake", "--build", "build"
+      system "cmake", "--install", "build"
+      system "make", "-C", "contrib/intervaltree", "install", "DESTDIR=", "PREFIX=#{buildpath}/vendor"
+      (buildpath/"vendor/include").install "contrib/tabixpp/tabix.hpp"
 
-      # libvcflib.a is installed into CMAKE_INSTALL_BINDIR
-      (buildpath/"vendor/bin").install "build_vcflib/contrib/WFA2-lib/libwfa2.a"
-      inreplace "meson.build" do |s|
-        s.sub! "find_library('libvcflib'", "\\0, dirs: ['#{buildpath}/vendor/bin']"
-        s.sub! "find_library('libwfa2'", "\\0, dirs: ['#{buildpath}/vendor/bin']"
-      end
+      ENV.append_path "LIBRARY_PATH", buildpath/"vendor/bin"
       ENV.append_to_cflags "-I#{buildpath}/vendor/include"
+      ENV.append_to_cflags "-I#{buildpath}/vendor/include/vcflib"
     end
 
-    # Workaround for ../src/BedReader.h:12:10: fatal error: 'IntervalTree.h' file not found
-    # Issue ref: https://github.com/freebayes/freebayes/issues/803
-    ENV.append_to_cflags "-I#{buildpath}/contrib/SeqLib/SeqLib"
-
-    system "meson", "setup", "build", "-Dcpp_std=c++14", *std_meson_args
+    # Set prefer_system_deps=false as we don't have formulae for these and some are not versioned/tagged
+    system "meson", "setup", "build", "-Dcpp_std=c++14", "-Dprefer_system_deps=false", *std_meson_args
     system "meson", "compile", "-C", "build", "--verbose"
     system "meson", "install", "-C", "build"
     pkgshare.install "test"