Add a package for Picard (#4398)

See the discussion about installing jar files in #4386.

Also installs a wrapper script that has explicit references to the
prerequisite java exe and to the jar file in it's final resting place.

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

@@ -0,0 +1,75 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+from shutil import copyfile
+import glob
+import os.path
+import re
+
+
+class Picard(Package):
+    """Picard is a set of command line tools for manipulating high-throughput
+       sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
+    """
+
+    homepage = "http://broadinstitute.github.io/picard/"
+    url      = "https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar"
+
+    # They started distributing a single jar file at v2.6.0, prior to
+    # that it was a .zip file with multiple .jar and .so files
+    version('2.9.2', '0449279a6a89830917e8bcef3a976ef7', expand=False,
+            url="https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar")
+    version('1.140', '308f95516d94c1f3273a4e7e2b315ec2',
+            url='https://github.com/broadinstitute/picard/releases/download/1.140/picard-tools-1.140.zip')
+
+    depends_on('jdk@8:', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        # The list of files to install varies with release...
+        # ... but skip the spack-{build.env}.out files.
+        files = [x for x in glob.glob("*") if not re.match("^spack-", x)]
+        for f in files:
+            install(f, 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__), "picard.sh")
+        script = join_path(prefix.bin, "picard")
+        copyfile(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = join_path(self.spec['jdk'].prefix, 'bin', 'java')
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('picard.jar', join_path(prefix.bin, 'picard.jar'),
+                    script, **kwargs)
+
+    def setup_environment(self, spack_env, run_env):
+        """The Picard docs suggest setting this as a convenience."""
+        run_env.prepend_path('PICARD',
+                             join_path(self.prefix, 'bin', 'picard.jar'))

var/spack/repos/builtin/packages/picard/picard.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the picard jar file
+java -jar picard.jar "$@"