pgdspider: new package (#5186)

* pgdspider: new package

* couple of fixes

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

@@ -0,0 +1,57 @@
+##############################################################################
+# 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 NOTICE and LICENSE files 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 *
+import os.path
+
+
+class Pgdspider(Package):
+    """"PGDSpider is a powerful automated data conversion tool for population
+        genetic and genomics programs"""
+
+    homepage = "http://www.cmpg.unibe.ch/software/PGDSpider"
+    url      = "http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider_2.1.1.2.zip"
+
+    version('2.1.1.2', '170e5b4a002277ff66866486da920693')
+
+    depends_on('java', type=('build', 'run'))
+    depends_on('bcftools')
+    depends_on('bwa')
+    depends_on('samtools')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = 'PGDSpider{0}-cli.jar'.format(self.version.up_to(1))
+        install(jar_file, prefix.bin)
+
+        script_sh = join_path(os.path.dirname(__file__), "pgdspider.sh")
+        script = prefix.bin.pgdspider
+        install(script_sh, script)
+        set_executable(script)
+
+        java = self.spec['java'].prefix.bin.java
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('pgdspider.jar', join_path(prefix.bin, jar_file),
+                    script, **kwargs)

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

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+#!/bin/sh
+# convenience wrapper for the astral jar file
+java $JAVA_ARGS $JAVA_OPTS -jar pgdspider.jar "$@"