From 46d8cb8913a782b7a244104b3b3be5d7957cd2f1 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Thu, 17 Aug 2017 11:21:56 -0500 Subject: paml: new package (#5142) --- var/spack/repos/builtin/packages/paml/package.py | 52 ++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 var/spack/repos/builtin/packages/paml/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/paml/package.py b/var/spack/repos/builtin/packages/paml/package.py new file mode 100644 index 0000000000..693d2b808b --- /dev/null +++ b/var/spack/repos/builtin/packages/paml/package.py @@ -0,0 +1,52 @@ +############################################################################## +# 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 Paml(MakefilePackage): + """PAML is a package of programs for phylogenetic analyses of DNA or + protein sewuences using maximum likelihood.""" + + homepage = "http://abacus.gene.ucl.ac.uk/software/paml.html" + url = "http://abacus.gene.ucl.ac.uk/software/paml4.9e.tgz" + + version('4.9e', 'ac5a062bfea1f4eaac79008434030acf') + + build_directory = 'src' + + def install(self, spec, prefix): + mkdirp(prefix.bin) + with working_dir(self.build_directory): + install('baseml', prefix.bin) + install('basemlg', prefix.bin) + install('chi2', prefix.bin) + install('codeml', prefix.bin) + install('evolver', prefix.bin) + install('infinitesites', prefix.bin) + install('mcmctree', prefix.bin) + install('pamp', prefix.bin) + install('yn00', prefix.bin) + install_tree('dat', prefix.dat) + install_tree('Technical', prefix.Technical) -- cgit v1.2.3-60-g2f50