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authorSimon Flood <simonflood@users.noreply.github.com>2018-10-08 22:02:12 +0100
committerLevi Baber <baberlevi@gmail.com>2018-10-08 16:02:12 -0500
commit84046b79b29cbf681a7ef0022077ab9fdf4ee2f4 (patch)
tree80dde0874402bb3668b0f195a90eadf6450e5a06
parentb2e255fe5a8432e1bfbd157910f5478e61cf884b (diff)
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New package: pplacer (#9112)
* New package: pplacer Simple package - copies files and directory out of a zip file * Update package.py
-rw-r--r--var/spack/repos/builtin/packages/pplacer/package.py46
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diff --git a/var/spack/repos/builtin/packages/pplacer/package.py b/var/spack/repos/builtin/packages/pplacer/package.py
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+++ b/var/spack/repos/builtin/packages/pplacer/package.py
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+##############################################################################
+# 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)