mrbayes: new package (#4757)

* mrbayes: new package

* fixing beagle version

* fixing typos

* fixing libbeagle dependency types

2 files changed, 119 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/libbeagle/package.py b/var/spack/repos/builtin/packages/libbeagle/package.py
new file mode 100644
index 0000000000..f459c5f738
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libbeagle/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# 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 Libbeagle(AutotoolsPackage):
+    """Beagle performs genotype calling, genotype phasing, imputation of
+       ungenotyped markers, and identity-by-descent segment detection."""
+
+    homepage = "https://github.com/beagle-dev/beagle-lib"
+    url      = "https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz"
+
+    version('2.1.2', '1107614e86f652f8ee45c1c92f2af3d4')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+
+    depends_on('subversion', type='build')
+    depends_on('pkg-config', type='build')
+
+    def url_for_version(self, version):
+        url = "https://github.com/beagle-dev/beagle-lib/archive/beagle_release_{0}.tar.gz"
+        return url.format(version.underscored)
diff --git a/var/spack/repos/builtin/packages/mrbayes/package.py b/var/spack/repos/builtin/packages/mrbayes/package.py
new file mode 100644
index 0000000000..05038b6931
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mrbayes/package.py
@@ -0,0 +1,72 @@
+##############################################################################
+# 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 Mrbayes(AutotoolsPackage):
+    """MrBayes is a program for Bayesian inference and model choice across a
+       wide range of phylogenetic and evolutionary models. MrBayes uses Markov
+       chain Monte Carlo (MCMC) methods to estimate the posterior distribution
+       of model parameters."""
+
+    homepage = "http://mrbayes.sourceforge.net"
+    url      = "https://downloads.sourceforge.net/project/mrbayes/mrbayes/3.2.6/mrbayes-3.2.6.tar.gz"
+
+    version('3.2.6', '95f9822f24be47b976bf87540b55d1fe')
+
+    variant('mpi', default=True, description='Enable MPI parallel support')
+    variant('beagle', default=True, description='Enable BEAGLE library for speed benefits')
+    variant('sse', default=True, description='Enable SSE in order to substantially speed up execution')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+
+    depends_on('libbeagle', when='+beagle')
+    depends_on('mpi', when='+mpi')
+
+    configure_directory = 'src'
+
+    def configure_args(self):
+        args = []
+        if '~beagle' in self.spec:
+            args.append('--with-beagle=no')
+        else:
+            args.append('--with-beagle=%s' % self.spec['libbeagle'].prefix)
+        if '~sse' in self.spec:
+            args.append('--enable-sse=no')
+        else:
+            args.append('--enable-sse=yes')
+        if '~mpi' in self.spec:
+            args.append('--enable-mpi=no')
+        else:
+            args.append('--enable-mpi=yes')
+        return args
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        with working_dir('src'):
+            install('mb', prefix.bin)