snphylo: new package (#7045)

* pushing partially done recipe for snphylo

* r-snphylo: try

* phylip: added version 3.697

* snphylo: updated package.py

* snphylo: flake8 error fixed

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

@@ -30,7 +30,7 @@ class Phylip(Package):
        inferring phylogenies (evolutionary trees)."""
 
     homepage = "http://evolution.genetics.washington.edu/phylip/"
-    url      = "http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz"
+    url      = "http://evolution.gs.washington.edu/phylip/download/phylip-3.697.tar.gz"
 
     version('3.697', '0e83d17fb4d668213603c86bc21d9012')
     version('3.696', 'dbe5abc26f6089ead3dba41c2db526ee')

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

@@ -0,0 +1,57 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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/spack/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 distutils.dir_util
+
+
+class Snphylo(Package):
+    """A pipeline to generate a phylogenetic tree from huge SNP data"""
+
+    homepage = "http://chibba.pgml.uga.edu/snphylo/"
+    url      = "http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz"
+
+    version('2016-02-04', '467660814965bc9bed6c020c05c0d3a6')
+
+    depends_on('python', type=('build', 'run'))
+    depends_on('r', type=('build', 'run'))
+    depends_on('r-phangorn', type=('build', 'run'))
+    depends_on('r-gdsfmt', type=('build', 'run'))
+    depends_on('r-snprelate', type=('build', 'run'))
+    depends_on('r-getopt', type=('build', 'run'))
+    depends_on('muscle')
+    depends_on('phylip')
+
+    def install(self, spec, prefix):
+        install_answer = ['y', 'y', 'y', 'y']
+        install_answer_input = 'spack-config.in'
+        with open(install_answer_input, 'w') as f:
+            f.writelines(install_answer)
+        with open(install_answer_input, 'r') as f:
+            bash = which('bash')
+            bash('./setup.sh', input=f)
+            distutils.dir_util.copy_tree(".", prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.spec.prefix)