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# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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('1.43.0', sha256='12ccd95a85bec3bb1564b8feabd244ea85413973740754803d01fc71ecb0a2c1')
version('1.42.1', sha256='6b61591dda289ac2d8361f9c1547ffbeeba3b9fbdff877dd286bad850bbd5539')
version('1.40.5', sha256='a0fbdfa68b966d7adc4560e3787506a0dad8b47b4b996c2663cd6c0b416d101a')
version('1.39.5', sha256='9f1cd691e9631a2ab7647b19eb59cd21ea643f29b22cde73d7f343372dfee342')
variant('vsearch', default=False, description='Use vsearch')
depends_on('boost')
depends_on('readline')
depends_on('vsearch', when='+vsearch', type='run')
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)
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