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-rw-r--r--var/spack/repos/builtin/packages/qorts/QoRTs.sh3
-rw-r--r--var/spack/repos/builtin/packages/qorts/package.py71
2 files changed, 74 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/qorts/QoRTs.sh b/var/spack/repos/builtin/packages/qorts/QoRTs.sh
new file mode 100644
index 0000000000..d847e76e05
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qorts/QoRTs.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the QoRTs jar file
+java -jar QoRTs.jar "$@"
diff --git a/var/spack/repos/builtin/packages/qorts/package.py b/var/spack/repos/builtin/packages/qorts/package.py
new file mode 100644
index 0000000000..bb71f15b8f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qorts/package.py
@@ -0,0 +1,71 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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/spack/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
+from shutil import copyfile
+
+
+class Qorts(RPackage):
+ """The QoRTs software package is a fast, efficient, and portable
+ multifunction toolkit designed to assist in the analysis, quality
+ control, and data management of RNA-Seq and DNA-Seq datasets. Its
+ primary function is to aid in the detection and identification of
+ errors, biases, and artifacts produced by high-throughput sequencing
+ technology."""
+
+ homepage = "https://github.com/hartleys/QoRTs"
+ url = "https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs_1.2.42.tar.gz"
+
+ version('1.2.42', '7d46162327b0da70bfe483fe2f2b7829')
+
+ depends_on('java', type='run')
+
+ resource(
+ name='QoRTs.jar',
+ url='https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs.jar',
+ md5='918df4291538218c12caa3ab98c535e9',
+ placement='jarfile',
+ expand=False
+ )
+
+ @run_after('install')
+ def install_jar(self):
+ install_tree(join_path(self.stage.source_path, 'jarfile'),
+ self.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__), "QoRTs.sh")
+ script = self.prefix.bin.QoRTs
+ copyfile(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 = {'backup': False}
+ filter_file('^java', java, script, **kwargs)
+ filter_file('QoRTs.jar', join_path(self.prefix.bin, 'QoRTs.jar'),
+ script, **kwargs)