new package: bref3 (#14256)

var/spack/repos/builtin/packages/bref3/bref.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+# convenience wrapper for the jar file
+java $JAVA_ARGS $JAVA_OPTS -jar bref.jar "$@"
+

var/spack/repos/builtin/packages/bref3/package.py

@@ -0,0 +1,46 @@
+# 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 Bref3(Package):
+    """Bref3: Converts from VCF format to bref3 format."""
+
+    homepage = "http://faculty.washington.edu/browning/beagle/beagle.html"
+
+    version('2019-11-25', sha256='969c0881050c4a48d19be9ea64bf49fa68c1403b69f9f739bbfd865dda639b2d', 
+            expand=False, url='http://faculty.washington.edu/browning/beagle/bref3.25Nov19.28d.jar')
+    version('2019-07-12', sha256='8a9c3b6c38e36ef4c05a61108f083005fd985026c67d75a8173088f88816a202',
+            expand=False, url='https://faculty.washington.edu/browning/beagle/bref3.12Jul19.0df.jar')
+    version('2018-01-27', sha256='4d32f0b6d536c88d5332d961309466c8c3dd9572907a3755450d26d7ba841083',
+            expand=False, url='https://faculty.washington.edu/browning/beagle/bref.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.
+
+        if self.version >= Version('2019'):
+            script = prefix.bin.bref3
+        else:
+            script = prefix.bin.bref
+
+        script_sh = join_path(os.path.dirname(__file__), "bref.sh")
+        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('bref.jar', join_path(prefix.bin, jar_file),
+                    script, **kwargs)