hap-ibd 1.0.0 (#1701)

Formula/hap-ibd.rb

@@ -0,0 +1,26 @@
+class HapIbd < Formula
+  # cite Zhou_2020: "https://doi.org/10.1016/j.ajhg.2020.02.010"
+  desc "Detect identity-by-descent segments in phased genotype data"
+  homepage "https://github.com/browning-lab/hap-ibd"
+  url "https://github.com/browning-lab/hap-ibd/archive/refs/tags/v1.0.0-15Jun23.92f.tar.gz"
+  version "1.0.0"
+  sha256 "9668be3580822a6da5c34fee4c04f05fa51b8471c339fc271a6404556ecc458d"
+  license "Apache-2.0"
+  head "https://github.com/browning-lab/hap-ibd.git", branch: "master"
+
+  depends_on "openjdk"
+
+  def install
+    system "#{Formula["openjdk"].bin}/javac", "-cp", "src/", "src/hapibd/HapIbdMain.java"
+    system "#{Formula["openjdk"].bin}/jar", "-cfe", "hap-ibd.jar", "hapibd.HapIbdMain", "-C", "src/", "."
+
+    libexec.install "hap-ibd.jar"
+    bin.write_jar_script libexec/"hap-ibd.jar", "hap-ibd"
+  end
+
+  test do
+    assert_predicate bin/"hap-ibd", :executable?
+    assert_predicate libexec/"hap-ibd.jar", :exist?
+    assert_match(/^Syntax: java -jar hap-ibd.jar\b/, shell_output("#{bin}/hap-ibd"))
+  end
+end