From 84046b79b29cbf681a7ef0022077ab9fdf4ee2f4 Mon Sep 17 00:00:00 2001 From: Simon Flood Date: Mon, 8 Oct 2018 22:02:12 +0100 Subject: New package: pplacer (#9112) * New package: pplacer Simple package - copies files and directory out of a zip file * Update package.py --- .../repos/builtin/packages/pplacer/package.py | 46 ++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 var/spack/repos/builtin/packages/pplacer/package.py 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) -- cgit v1.2.3-70-g09d2