Merge pull request Homebrew#225177 from ankane/breseq

breseq 0.39.0 (new formula)

Author: BrewTestBot

Formula/b/breseq.rb

@@ -0,0 +1,51 @@
+class Breseq < Formula
+  desc "Computational pipeline for finding mutations in short-read DNA resequencing data"
+  homepage "https://barricklab.org/breseq"
+  url "https://github.com/barricklab/breseq/archive/refs/tags/v0.39.0.tar.gz"
+  sha256 "5aa1bd9af71899e1358cfb9b8440c16cc908f185d9178a401a5a4d3f0c7ee861"
+  license all_of: ["GPL-2.0-or-later", "MIT", "BSD-3-Clause"]
+  head "https://github.com/barricklab/breseq.git", branch: "master"
+
+  bottle do
+    sha256 cellar: :any_skip_relocation, arm64_sequoia: "f22120bae403eb392bec70333093e7176e565853bf5108b51ed37b82a8b39d54"
+    sha256 cellar: :any_skip_relocation, arm64_sonoma:  "a5d0b6591968d4b5747cf81d8f377560da5e8b2633d401d5e60f36e954655e49"
+    sha256 cellar: :any_skip_relocation, arm64_ventura: "251cb721ac1cedfb266a35557af31efc3964d9265c302c21186173c4089c5a3e"
+    sha256 cellar: :any_skip_relocation, sonoma:        "f071fdaf4fb3b7b454b94674075cabe7bed6bbc630b5e3979971f62a35de4401"
+    sha256 cellar: :any_skip_relocation, ventura:       "a7c5e18cc7968fd3e50450807eb1d84d2e1074b920e5a89011033c017621d248"
+    sha256 cellar: :any_skip_relocation, x86_64_linux:  "fecf53100efc095e8c48e3be539d2d40d12f285983ba02d64333326b3acc4040"
+  end
+
+  depends_on "autoconf" => :build
+  depends_on "automake" => :build
+  depends_on "libtool" => :build
+  depends_on "bowtie2"
+  depends_on "r"
+
+  uses_from_macos "zlib"
+
+  def install
+    system "autoreconf", "--force", "--install", "--verbose"
+    system "./configure", "--disable-silent-rules", *std_configure_args
+    system "make"
+    system "make", "install"
+  end
+
+  test do
+    resource "homebrew-test-gbk" do
+      url "https://raw.githubusercontent.com/barricklab/breseq/refs/tags/v0.39.0/tests/data/REL606/REL606.fragment.gbk"
+      sha256 "0e6edf3df46da73db9d07622316e0b9617e7a95faf87589bb0a7bc2393e2d92e"
+    end
+
+    resource "homebrew-test-fastq" do
+      url "https://raw.githubusercontent.com/barricklab/breseq/refs/tags/v0.39.0/tests/data/REL606/REL606.fragment.2.fastq"
+      sha256 "79775ab79421d43b41087f256f99f38681af5421d1303b86e6e92a471edbb0fb"
+    end
+
+    testpath.install resource("homebrew-test-gbk")
+    testpath.install resource("homebrew-test-fastq")
+
+    assert_match version.to_s, shell_output("#{bin}/breseq --version")
+    system bin/"breseq", "-r", "REL606.fragment.gbk", "REL606.fragment.2.fastq"
+    assert_path_exists "output"
+  end
+end