add package Feature/sentieon (#9557)

* added package sentieon

* change file location

* updated spack header license and added license_vars

* fixed flake8 error

* fixed license header

* fix license header

* license

* added import os.path

* edits

* flake8 edits

1 files changed, 39 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/sentieon-genomics/package.py b/var/spack/repos/builtin/packages/sentieon-genomics/package.py
new file mode 100644
index 0000000000..e860a76bef
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sentieon-genomics/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 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)
+
+import os.path
+from spack import *
+
+
+class SentieonGenomics(Package):
+    """Sentieon provides complete solutions for secondary DNA analysis.
+    Our software improves upon BWA, GATK, Mutect, and Mutect2 based pipelines.
+    The Sentieon tools are deployable on any CPU-based computing system.
+    Please set the path to the sentieon license server with:
+
+    export SENTIEON_LICENSE=[FQDN]:[PORT]
+
+    Note: A manual download is required.
+    Spack will search your current directory for the download file.
+    Alternatively, add this file to a mirror so that Spack can find it.
+    For instructions on how to set up a mirror, see
+    http://spack.readthedocs.io/en/latest/mirrors.html"""
+
+    homepage = "https://www.sentieon.com/"
+    url      = "file://{0}/sentieon-genomics-201808.01.tar.gz".format(os.getcwd())
+
+    version('201808.01', sha256='6d77bcd5a35539549b28eccae07b19a3b353d027720536e68f46dcf4b980d5f7')
+
+    # Licensing.
+    license_require = True
+    license_vars = ['SENTIEON_LICENSE']
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('doc', prefix.doc)
+        install_tree('etc', prefix.etc)
+        install_tree('lib', prefix.lib)
+        install_tree('libexec', prefix.libexec)
+        install_tree('share', prefix.share)