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authorAudrey Thoma <las_thoma15@iastate.edu>2017-08-23 08:34:12 -0500
committerAdam J. Stewart <ajstewart426@gmail.com>2017-08-23 08:34:12 -0500
commit359b21c888c923ef61b4680cdbd00e3781a9d78b (patch)
tree91673f1175ee0ee16e7a5016b77019535e4f85e3
parent0daa639788b7bc0b0da14001308176ba1c8c3856 (diff)
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pgdspider: new package (#5186)
* pgdspider: new package * couple of fixes
-rw-r--r--var/spack/repos/builtin/packages/pgdspider/package.py57
-rw-r--r--var/spack/repos/builtin/packages/pgdspider/pgdspider.sh3
2 files changed, 60 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/pgdspider/package.py b/var/spack/repos/builtin/packages/pgdspider/package.py
new file mode 100644
index 0000000000..60dfdc12f4
--- /dev/null
+++ b/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)
diff --git a/var/spack/repos/builtin/packages/pgdspider/pgdspider.sh b/var/spack/repos/builtin/packages/pgdspider/pgdspider.sh
new file mode 100644
index 0000000000..5ac0f66c08
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pgdspider/pgdspider.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the astral jar file
+java $JAVA_ARGS $JAVA_OPTS -jar pgdspider.jar "$@"