8000 freebayes 1.3.10 · Homebrew/homebrew-core@e5e3b3e · GitHub
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freebayes 1.3.10
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‎Formula/f/freebayes.rb

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@@ -3,8 +3,8 @@ class Freebayes < Formula
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homepage "https://github.com/freebayes/freebayes"
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# pull from git tag to get submodules
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url "https://github.com/freebayes/freebayes.git",
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tag: "v1.3.9",
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revision: "ab36d1f789c039ba872f5d911ce6ff09952dc329"
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tag: "v1.3.10",
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revision: "b0d8efd9fa7f6612c883ec5ff79e4d17a0c29993"
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license "MIT"
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head "https://github.com/freebayes/freebayes.git", branch: "master"
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@@ -28,73 +28,30 @@ class Freebayes < Formula
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sha256 x86_64_linux: "8b76cc3e3db9575510c456b74286a1f5732e5495b3c1232311a2c0c220fc7e0f"
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end
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depends_on "cmake" => :build # for vcflib
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depends_on "cmake" => :build
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depends_on "meson" => :build
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depends_on "ninja" => :build
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depends_on "pkgconf" => :build
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depends_on "pybind11" => :build # for vcflib
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depends_on "simde" => :build
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depends_on "wfa2-lib" => :build # for vcflib
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depends_on "xz" => :build # for vcflib
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depends_on "wfa2-lib" => :build
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depends_on "htslib"
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depends_on "tabixpp"
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uses_from_macos "bzip2" => :build # for vcflib
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uses_from_macos "zlib" => :build # for vcflib
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uses_from_macos "llvm" => :build
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on_macos do
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depends_on "libomp" => :build # for vcflib
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end
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resource "vcflib" do
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url "https://github.com/vcflib/vcflib/releases/download/v1.0.12/vcflib-1.0.12-src.tar.gz"
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sha256 "cb1e78d675f06ae3b22ffed7e1dea317e4c7f826e51e5b5dabd80240efbe1019"
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# Backport fix for using external `wfa2-lib`
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patch do
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url "https://github.com/vcflib/vcflib/commit/5e4edec2fba5d5a51dae7a9fe48d0252ade53857.patch?full_index=1"
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sha256 "e7d6d433d837dd823916ef91fe0165bf4ba4f05c52fd4c9517aef7f80653a2a8"
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end
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# Apply open PR to help find `wfa2-lib` include directory
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# PR ref: https://github.com/vcflib/vcflib/pull/413
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patch do
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url "https://github.com/vcflib/vcflib/commit/9f9237ff0e6b4887f0edfc88587957aa736ced7b.patch?full_index=1"
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sha256 "bede43d22b4b47141cd90edc4df90f65b9ac41e9598c2b05b2fe7fa84ea51aa8"
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end
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end
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# Apply open PR to help Meson locate vcflib and wfa2 libraries
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# PR ref: https://github.com/freebayes/freebayes/pull/822
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patch do
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url "https://github.com/freebayes/freebayes/commit/b458396e1acbad3983c70c202a6db2b3711a8eac.patch?full_index=1"
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sha256 "b5c7d855d4d66c6c96dada307e82ccbf0b6904a25928c4f3e163f52e178b7907"
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end
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# Apply open PR to fix build when using git submodules
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# PR ref: https://github.com/freebayes/freebayes/pull/823
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patch do
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url "https://github.com/freebayes/freebayes/commit/35eeacb6468fdce25233a33f7216f4e776d381f9.patch?full_index=1"
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sha256 "1b6f0bb1e369a4b11e9a7754f3b789035b39cc5d9e3dbbac84fde21893f0d9be"
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resource "intervaltree" do
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url "https://github.com/ekg/intervaltree/archive/refs/tags/v0.1.tar.gz"
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sha256 "7ba41f164a98bdcd570f1416fde1634b23d3b0d885b11ccebeec76f58810c307"
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end
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def install
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resource("vcflib").stage do
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rm_r(["contrib/WFA2-lib", "contrib/tabixpp/htslib"]) # avoid bundled libraries
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system "cmake", "-S", ".", "-B", "build",
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"-DBUILD_DOC=OFF",
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"-DBUILD_ONLY_LIB=ON",
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"-DZIG=OFF",
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*std_cmake_args(install_prefix: buildpath/"vendor")
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system "cmake", "--build", "build"
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system "cmake", "--install", "build"
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system "make", "-C", "contrib/intervaltree", "install", "DESTDIR=", "PREFIX=#{buildpath}/vendor"
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(buildpath/"vendor/include").install "contrib/tabixpp/tabix.hpp"
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# add contrib to include directories
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inreplace "meson.build", "incdir = include_directories(", "incdir = include_directories('contrib',"
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ENV.append_path "LIBRARY_PATH", buildpath/"vendor/bin"
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ENV.append_to_cflags "-I#{buildpath}/vendor/include"
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ENV.append_to_cflags "-I#{buildpath}/vendor/include/vcflib"
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end
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# install intervaltree
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(buildpath/"contrib/intervaltree").install resource("intervaltree")
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# add tabixpp to include directories
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ENV.append_to_cflags "-I#{Formula["tabixpp"].opt_include} -L#{Formula["tabixpp"].opt_lib} -ltabix"
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# Set prefer_system_deps=false as we don't have formulae for these and some are not versioned/tagged
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system "meson", "setup", "build", "-Dcpp_std=c++14", "-Dprefer_system_deps=false", *std_meson_args

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