New package: pplacer (#9112)

* New package: pplacer

Simple package - copies files and directory out of a zip file

* Update package.py

1 files changed, 46 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/pplacer/package.py b/var/spack/repos/builtin/packages/pplacer/package.py
new file mode 100644
index 0000000000..bc67736d03
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pplacer/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# 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 *
+
+
+class Pplacer(Package):
+    """Pplacer places query sequences on a fixed reference phylogenetic tree
+       to maximize phylogenetic likelihood or posterior probability according
+       to a reference alignment. Pplacer is designed to be fast, to give
+       useful information about uncertainty, and to offer advanced
+       visualization and downstream analysis.
+    """
+
+    homepage = "http://matsen.fhcrc.org/pplacer/"
+    url      = "https://github.com/matsen/pplacer/releases/download/v1.1.alpha19/pplacer-linux-v1.1.alpha19.zip"
+
+    version('1.1.alpha19', 'e6b78604882d41d4bf13592c7edebfa2')
+
+    def install(self, spec, prefix):
+        install_tree('scripts', prefix.bin)
+        force_remove(join_path(prefix.bin, 'setup.py'))
+        install('guppy', prefix.bin)
+        install('pplacer', prefix.bin)
+        install('rppr', prefix.bin)