From a10253a667406209f10be76459a3f34ce396899f Mon Sep 17 00:00:00 2001
From: xfzhao <xfzhao@iastate.edu>
Date: Sat, 21 Dec 2019 18:22:56 -0600
Subject: new module beagle (#14257)

---
 var/spack/repos/builtin/packages/beagle/beagle.sh  |  4 ++
 var/spack/repos/builtin/packages/beagle/package.py | 43 ++++++++++++++++++++++
 2 files changed, 47 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/beagle/beagle.sh
 create mode 100644 var/spack/repos/builtin/packages/beagle/package.py

diff --git a/var/spack/repos/builtin/packages/beagle/beagle.sh b/var/spack/repos/builtin/packages/beagle/beagle.sh
new file mode 100644
index 0000000000..58093103f3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/beagle/beagle.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+# convenience wrapper for the jar file
+java $JAVA_ARGS $JAVA_OPTS -jar beagle.jar "$@"
+
diff --git a/var/spack/repos/builtin/packages/beagle/package.py b/var/spack/repos/builtin/packages/beagle/package.py
new file mode 100644
index 0000000000..391807db42
--- /dev/null
+++ b/var/spack/repos/builtin/packages/beagle/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os.path
+
+
+class Beagle(Package):
+    """Beagle is a software package for phasing genotypes and for imputing
+       ungenotyped markers."""
+
+    homepage = "http://faculty.washington.edu/browning/beagle/beagle.html"
+
+    version('5.1', sha256='994f926a4ec0eac665631f37c4a961d3f75c966c71841079275364013c90996c',
+            expand=False, url='http://faculty.washington.edu/browning/beagle/beagle.25Nov19.28d.jar')
+    version('5.0', sha256='8390fe18b53786b676b67dddae6d1c086d6225e518f6a82047f4138196b48621',
+            expand=False, url='https://faculty.washington.edu/browning/beagle/beagle.12Jul19.0df.jar')
+    version('4.1', sha256='6c94610b278fc108c3e80b1134226911be1fc92b7d378ba648ac3eb97c5a3207',
+            expand=False, url='https://faculty.washington.edu/browning/beagle/beagle.27Jan18.7e1.jar')
+
+    depends_on('java@8', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = os.path.basename(self.stage.archive_file)
+        install(jar_file, prefix.bin)
+
+        # Set up a helper script to call java on the jar file,
+        # explicitly codes the path for java and the jar file.
+        script_sh = join_path(os.path.dirname(__file__), "beagle.sh")
+        script = prefix.bin.beagle
+        install(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = self.spec['java'].prefix.bin.java
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('beagle.jar', join_path(prefix.bin, jar_file),
+                    script, **kwargs)
-- 
cgit v1.2.3-60-g2f50