From 6abe8e7d9114f0f202a5ba722f9877b6b1cc5a55 Mon Sep 17 00:00:00 2001
From: Audrey Thoma <las_thoma15@iastate.edu>
Date: Fri, 18 Aug 2017 09:36:35 -0500
Subject: [PATCH] parsimonator: new package (#5143)

* parsimonator: new package

* adding variant conflict
---
 .../builtin/packages/parsimonator/package.py  | 65 +++++++++++++++++++
 1 file changed, 65 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/parsimonator/package.py

diff --git a/var/spack/repos/builtin/packages/parsimonator/package.py b/var/spack/repos/builtin/packages/parsimonator/package.py
new file mode 100644
index 0000000000..5b979f23e3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parsimonator/package.py
@@ -0,0 +1,65 @@
+##############################################################################
+# 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 *
+
+
+class Parsimonator(MakefilePackage):
+    """Parsimonator is a no-frills light-weight implementation for building
+       starting trees under parsimony for RAxML"""
+
+    homepage = "http://www.exelixis-lab.org/"
+    url      = "https://github.com/stamatak/Parsimonator-1.0.2"
+
+    version('1.0.2', git='https://github.com/stamatak/Parsimonator-1.0.2.git', commit='78368c6ab1e9adc7e9c6ec9256dd7ff2a5bb1b0a')
+
+    variant('sse', default=True, description='Enable SSE in order to substantially speed up execution')
+    variant('avx', default=False, description='Enable AVX in order to substantially speed up execution')
+
+    conflicts('+avx', when='+sse')
+
+    @property
+    def makefile_file(self):
+        if '+sse' in self.spec:
+            return 'Makefile.SSE3.gcc'
+        elif '+avx' in self.spec:
+            return 'Makefile.AVX.gcc'
+        else:
+            return 'Makefile.gcc'
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter(self.makefile_file)
+        makefile.filter('CC = gcc', 'CC = %s' % spack_cc)
+
+    def build(self, spec, prefix):
+        make('-f', self.makefile_file)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        if '+sse' in spec:
+            install('parsimonator-SSE3', prefix.bin)
+        elif '+avx' in spec:
+            install('parsimonator-AVX', prefix.bin)
+        else:
+            install('parsimonator', prefix.bin)