41 lines
1.6 KiB
Python
41 lines
1.6 KiB
Python
# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import re
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from spack.package import *
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class Soapdenovo2(MakefilePackage):
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"""SOAPdenovo is a novel short-read assembly method that can build a de
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novo draft assembly for the human-sized genomes. The program is
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specially designed to assemble Illumina GA short reads. It creates
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new opportunities for building reference sequences and carrying out
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accurate analyses of unexplored genomes in a cost effective way."""
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homepage = "https://github.com/aquaskyline/SOAPdenovo2"
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url = "https://github.com/aquaskyline/SOAPdenovo2/archive/r240.tar.gz"
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maintainers("snehring")
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license("GPL-3.0-only")
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version("242", sha256="a0043ceb41bc17a1c3fd2b8abe4f9029a60ad3edceb2b15af3c2cfabd36aa11b")
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version("240", sha256="cc9e9f216072c0bbcace5efdead947e1c3f41f09baec5508c7b90f933a090909")
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def flag_handler(self, name, flags):
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if name.lower() == "cflags" and self.spec.satisfies("%gcc@10:"):
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flags.append("-fcommon")
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if name.lower() in ["cflags", "cxxflags", "cppflags"]:
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opt_flag = re.compile("-O.*")
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# This package cannot compile with any optimization flag other
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# than the -O3 specified in the makefile
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flags = [f for f in flags if not opt_flag.match(f)]
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return (flags, None, None)
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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install("SOAPdenovo-63mer", prefix.bin)
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install("SOAPdenovo-127mer", prefix.bin)
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