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# Copyright 2013-2023 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 *
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"
license("GPL-3.0-or-later")
version("1.48.0", sha256="9494406abd8d14b821782ab9db811f045ded9424f28f01234ee6764d4e78941d")
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")
maintainers("snehring")
variant(
"boost",
default=True,
description="Build with boost support (allow make.contigs to read gz files).",
)
variant("hdf5", default=False, description="Build with hdf5 support", when="@1.41.0:")
variant(
"gsl", default=False, description="Build with the gnu scientific libaries", when="@1.43.0:"
)
depends_on("boost+iostreams+filesystem+system", when="+boost")
depends_on("gsl", when="+gsl")
depends_on("hdf5+cxx", when="+hdf5")
depends_on("readline")
depends_on("vsearch@2.13.5:", type="run")
depends_on("usearch", type="run")
depends_on("zlib-api", when="+boost")
def edit(self, spec, prefix):
filter_file(r"^.*DMOTHUR_TOOLS.*$", "", "Makefile")
filter_file(r"^.*DMOTHUR_FILES.*$", "", "Makefile")
filter_file(r"(\$\(skipUchime\))", r"\1, source/", "Makefile")
if spec.satisfies("@1.40.5"):
filter_file(
r"^(#define writer_h)", "\\1 \n#include<memory>", join_path("source", "writer.h")
)
# this includes the public domain uchime, which needs work to
# compile on newer compilers we'll use what's in usearch
filter_file(" uchime", "", "Makefile")
if spec.satisfies("+boost"):
filter_file(r"USEBOOST \?=.*$", "USEBOOST = yes", "Makefile")
filter_file(
r"^BOOST_LIBRARY_DIR .*$",
"BOOST_LIBRARY_DIR=%s" % self.spec["boost"].prefix.lib,
"Makefile",
)
filter_file(
r"BOOST_INCLUDE_DIR .*$",
"BOOST_INCLUDE_DIR=%s" % self.spec["boost"].prefix.include,
"Makefile",
)
if spec.satisfies("+hdf5"):
filter_file(r"USEHDF5 \?=.*$", "USEHDF5 = yes", "Makefile")
filter_file(
r"^HDF5_LIBRARY_DIR \?=.*$",
"HDF5_LIBRARY_DIR = " + spec["hdf5"].prefix.lib,
"Makefile",
)
filter_file(
r"^HDF5_INCLUDE_DIR \?=.*$",
"HDF5_INCLUDE_DIR = " + spec["hdf5"].prefix.include,
"Makefile",
)
if spec.satisfies("+gsl"):
filter_file(r"^USEGSL \?=.*$", "USEGSL = yes", "Makefile")
filter_file(
r"GSL_LIBRARY_DIR \?=.*$",
"GSL_LIBRARY_DIR = " + spec["gsl"].prefix.lib,
"Makefile",
)
filter_file(
r"GSL_INCLUDE_DIR \?=.*$",
"GSL_INCLUDE_DIR = " + spec["gsl"].prefix.include,
"Makefile",
)
def install(self, spec, prefix):
mkdirp(prefix.bin)
install("mothur", prefix.bin)
install_tree("source", prefix.include)
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