From 518993431d9c557bad52795ce1d0be0fa7c1219e Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Thu, 10 Aug 2017 18:09:40 -0500 Subject: mothur: new package (#5055) * mothur: new package * fixing mpi things --- var/spack/repos/builtin/packages/mothur/package.py | 59 ++++++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 var/spack/repos/builtin/packages/mothur/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mothur/package.py b/var/spack/repos/builtin/packages/mothur/package.py new file mode 100644 index 0000000000..0caf0bc1f9 --- /dev/null +++ b/var/spack/repos/builtin/packages/mothur/package.py @@ -0,0 +1,59 @@ +############################################################################## +# 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 Mothur(MakefilePackage): + """This project seeks to develop a single piece of open-source, expandable + software to fill the bioinformatics needs of the microbial ecology + community.""" + + homepage = "https://github.com/mothur/mothur" + url = "https://github.com/mothur/mothur/archive/v1.39.5.tar.gz" + + version('1.39.5', '1f826ea4420e6822fc0db002c5940b92') + + variant('mpi', default=True, description='Enable MPI parallel support') + + depends_on('mpi', when='+mpi') + depends_on('boost') + depends_on('readline') + + def edit(self, spec, prefix): + makefile = FileFilter('Makefile') + makefile.filter('BOOST_LIBRARY_DIR=\"\\\"Enter_your_boost_library_path' + '_here\\\"\"', 'BOOST_LIBRARY_DIR=%s' % + self.spec['boost'].prefix.lib) + makefile.filter('BOOST_INCLUDE_DIR=\"\\\"Enter_your_boost_include_path' + '_here\\\"\"', 'BOOST_INCLUDE_DIR=%s' % + self.spec['boost'].prefix.include) + makefile.filter('MOTHUR_FILES=\"\\\"Enter_your_default_path_' + 'here\\\"\"', 'MOTHUR_FILES=%s' % prefix) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('mothur', prefix.bin) + install('uchime', prefix.bin) + install_tree('source', prefix.include) -- cgit v1.2.3-60-g2f50