Merge pull request Homebrew#196489 from Homebrew/freebayes-1.3.8

freebayes 1.3.8
devcode1981 · Nov 3, 2024 · 1606610 · 1606610
2 parents 9ef27a3 + da50516
commit 1606610
Showing 1 changed file with 65 additions and 10 deletions.
diff --git a/Formula/f/freebayes.rb b/Formula/f/freebayes.rb
@@ -1,12 +1,44 @@
 class Freebayes < Formula
   desc "Bayesian haplotype-based genetic polymorphism discovery and genotyping"
   homepage "https://github.com/freebayes/freebayes"
-  url "https://github.com/freebayes/freebayes.git",
-      tag:      "v1.3.7",
-      revision: "ae60517162d34ab6217bd6c58e2b71551abacac2"
   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
@@ -18,13 +50,12 @@ class Freebayes < Formula
   end
 
   bottle do
-    sha256 cellar: :any, arm64_sonoma:   "86e8ecdd554dd65c305d5c3a4a77199712a9135b0b3fb2c592ace85e725c4d11"
-    sha256 cellar: :any, arm64_ventura:  "9f39d67a92d9e832723820b80cb4fa43ba7e2337887ef689fa43340424c77007"
-    sha256 cellar: :any, arm64_monterey: "1d03d1fcb588e8e5f96d32c6ad511e46a61712d1a4521623f53ad8b9ded2727b"
-    sha256 cellar: :any, sonoma:         "8faa87eff6dcab27a9799df3fb4abbfe7e137db29c6edac31fa91ff65b8d0a37"
-    sha256 cellar: :any, ventura:        "dd99fa0c8d6c01e68341e49ff4c13e686661d7d2f33806b00be261f9284ade29"
-    sha256 cellar: :any, monterey:       "4379827c288c32cc19ab7aa290b2f724254e3538d2f30288c5f1c3110aee705c"
-    sha256               x86_64_linux:   "d2b3b2c133c9f59c8a29a77e5a60b933a63ae83c664b62ddd0802844623a9bc6"
+    sha256 cellar: :any, arm64_sequoia: "42919ea368e7fb300680e17b7eb783e61eaa251c8b1492d2eba3e9db068bf3e8"
+    sha256 cellar: :any, arm64_sonoma:  "c367f0574466d1c538750aeed89d68b2066280be424fbfdd8f33f92ae6f3e538"
+    sha256 cellar: :any, arm64_ventura: "58b47ea65fc8b8fd2bcedad4b67e9edb1f41781679ddbd2f2d7d214a1e3eaabc"
+    sha256 cellar: :any, sonoma:        "d6c0009f7ed19acbfe3d93a83fe4a1ec6d1c21867f67ad037bfda62c56394122"
+    sha256 cellar: :any, ventura:       "b2631095db533474d1e6ce81dc00412cbf2c378bcd9cec40959b029aa8e9a8f4"
+    sha256               x86_64_linux:  "056ef004633b4ad83902199054e990313f0e2654455ebe17f822b28d5a7add9a"
   end
 
   depends_on "meson" => :build
@@ -36,6 +67,30 @@ class Freebayes < Formula
   uses_from_macos "zlib"
 
   def install
+    if build.stable?
+      resources.each { |r| (buildpath/r.name).install r }
+
+      system "cmake", "-S", "contrib/vcflib", "-B", "build_vcflib",
+                      "-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"
+
+      # 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_to_cflags "-I#{buildpath}/vendor/include"
+    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
     system "meson", "compile", "-C", "build", "--verbose"
     system "meson", "install", "-C", "build"