Add package for freebayes (#4718)

* Add package for freebayes

* Don't include url, must use git info.

* Fix flake8 complaints

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

@@ -0,0 +1,51 @@
+##############################################################################
+# 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 Freebayes(MakefilePackage):
+    """Bayesian haplotype-based genetic polymorphism discovery and
+       genotyping."""
+
+    homepage = "https://github.com/ekg/freebayes"
+
+    version('1.1.0', git='https://github.com/ekg/freebayes.git',
+            commit='39e5e4bcb801556141f2da36aba1df5c5c60701f',
+            submodules=True)
+
+    depends_on('cmake', type='build')
+    depends_on('zlib')
+
+    parallel = False
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        b = prefix.bin
+        makefile.filter('cp bin/freebayes bin/bamleftalign /usr/local/bin/',
+                        'cp bin/freebayes bin/bamleftalign {0}'.format(b))
+
+    @run_before('install')
+    def make_prefix_dot_bin(self):
+        mkdir(prefix.bin)