raxml: new package (#4777)

* raxml: new package

* changed compiler variable

* removing if statement regarding intel compiler

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

@@ -0,0 +1,107 @@
+##############################################################################
+# 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 glob
+
+
+class Raxml(Package):
+    """RAxML (Randomized Axelerated Maximum Likelihood) is a program for
+       sequential and parallel Maximum Likelihood based inference of large
+       phylogenetic trees."""
+
+    homepage = "https://sco.h-its.org/exelixis/web/software/raxml"
+    url      = "https://github.com/stamatak/standard-RAxML/archive/v8.2.11.tar.gz"
+
+    version('8.2.11', '6bd5c4e1f93003ccf13c9b59a5d080ab')
+
+    variant('mpi', default=True, description='Enable MPI parallel support')
+    variant('pthreads', default=False, description='Enable pthreads version')
+    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')
+
+    depends_on('mpi', when='+mpi')
+
+    # Compiles with either GCC or ICC.
+    conflicts('%cce')
+    conflicts('%clang')
+    conflicts('%nag')
+    conflicts('%pgi')
+    conflicts('%xl')
+    conflicts('%xl_r')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        files = glob.iglob("Makefile.*")
+        for file in files:
+            makefile = FileFilter(file)
+            makefile.filter('gcc', spack_cc)
+
+        if '+mpi' and '+avx' and '+pthreads' in spec:
+            make('-f', 'Makefile.AVX.HYBRID.gcc')
+            install('raxmlHPC-HYBRID-AVX', prefix.bin)
+
+        elif '+mpi' and '+sse' and '+pthreads' in spec:
+            make('-f', 'Makefile.SSE3.HYBRID.gcc')
+            install('raxmlHPC-HYBRID-SSE3', prefix.bin)
+
+        elif '+mpi' and '+pthreads' in spec:
+            make('-f', 'Makefile.HYBRID.gcc')
+            install('raxmlHPC-HYBRID', prefix.bin)
+
+        elif '+mpi' and '+avx' in spec:
+            make('-f', 'Makefile.AVX.MPI.gcc')
+            install('raxmlHPC-MPI-AVX', prefix.bin)
+
+        elif '+mpi' and '+sse' in spec:
+            make('-f', 'Makefile.SSE3.MPI.gcc')
+            install('raxmlHPC-MPI-SSE3', prefix.bin)
+
+        elif '+mpi' in spec:
+            make('-f', 'Makefile.MPI.gcc')
+            install('raxmlHPC-MPI', prefix.bin)
+
+        elif '+pthreads' and '+avx' in spec:
+            make('-f', 'Makefile.AVX.PTHREADS.gcc')
+            install('raxmlHPC-PTHREADS-AVX', prefix.bin)
+
+        elif '+pthreads' and '+sse' in spec:
+            make('-f', 'Makefile.SSE3.PTHREADS.gcc')
+            install('raxmlHPC-PTHREADS-SSE3', prefix.bin)
+
+        elif '+pthreads' in spec:
+            make('-f', 'Makefile.PTHREADS.gcc')
+            install('raxmlHPC-PTHREADS', prefix.bin)
+
+        elif '+sse' in spec:
+            make('-f', 'Makefile.SSE3.gcc')
+            install('raxmlHPC-SSE3', prefix.bin)
+
+        elif '+avx' in spec:
+            make('-f', 'Makefile.AVX.gcc')
+            install('raxmlHPC-AVX', prefix.bin)
+
+        else:
+            make('-f', 'Makefile.gcc')
+            install('raxmlHPC', prefix.bin)