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# Copyright 2013-2022 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.package import *
from spack.pkg.builtin.boost import Boost
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("1.46.1", sha256="29b500b3c92d726cde34922f697f2e47f0b7127d76d9a6fb167cc2b8ba3d00fd")
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")
# TODO: replace this with an explicit list of components of Boost,
# for instance depends_on('boost +filesystem')
# See https://github.com/spack/spack/pull/22303 for reference
depends_on(Boost.with_default_variants)
depends_on("readline")
depends_on("vsearch@2.13.3", 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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