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-rw-r--r--var/spack/repos/builtin/packages/libbeagle/package.py47
-rw-r--r--var/spack/repos/builtin/packages/mrbayes/package.py72
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)