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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)
import re
from spack.package import *
class Soapdenovo2(MakefilePackage):
"""SOAPdenovo is a novel short-read assembly method that can build a de
novo draft assembly for the human-sized genomes. The program is
specially designed to assemble Illumina GA short reads. It creates
new opportunities for building reference sequences and carrying out
accurate analyses of unexplored genomes in a cost effective way."""
homepage = "https://github.com/aquaskyline/SOAPdenovo2"
url = "https://github.com/aquaskyline/SOAPdenovo2/archive/r240.tar.gz"
maintainers("snehring")
license("GPL-3.0-only")
version("242", sha256="a0043ceb41bc17a1c3fd2b8abe4f9029a60ad3edceb2b15af3c2cfabd36aa11b")
version("240", sha256="cc9e9f216072c0bbcace5efdead947e1c3f41f09baec5508c7b90f933a090909")
def flag_handler(self, name, flags):
if name.lower() == "cflags" and self.spec.satisfies("%gcc@10:"):
flags.append("-fcommon")
if name.lower() in ["cflags", "cxxflags", "cppflags"]:
opt_flag = re.compile("-O.*")
# This package cannot compile with any optimization flag other
# than the -O3 specified in the makefile
flags = [f for f in flags if not opt_flag.match(f)]
return (flags, None, None)
def install(self, spec, prefix):
mkdirp(prefix.bin)
install("SOAPdenovo-63mer", prefix.bin)
install("SOAPdenovo-127mer", prefix.bin)
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