44 lines
1.6 KiB
Python
44 lines
1.6 KiB
Python
# Copyright 2013-2023 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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from spack.package import *
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class SoapdenovoTrans(MakefilePackage):
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"""SOAPdenovo-Trans is a de novo transcriptome assembler basing on the
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SOAPdenovo framework, adapt to alternative splicing and different
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expression level among transcripts."""
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homepage = "https://github.com/aquaskyline/SOAPdenovo-Trans"
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url = "https://github.com/aquaskyline/SOAPdenovo-Trans/archive/1.0.4.tar.gz"
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maintainers("snehring")
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version("1.0.5", sha256="c1903c0d81142270db95916e2833400f72c4841b5c9194f182c19ebda418936f")
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version("1.0.4", sha256="378a54cde0ebe240fb515ba67197c053cf95393645c1ae1399b3a611be2a9795")
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depends_on("zlib", type="link")
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depends_on("samtools@0.1.8", type="link", when="target=aarch64:")
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build_directory = "src"
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def edit(self, spec, prefix):
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with working_dir(self.build_directory):
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makefile = FileFilter("Makefile")
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makefile.filter(
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"CFLAGS= -O3 -fomit-frame-pointer -static",
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"CFLAGS= -O3 -fomit-frame-pointer",
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)
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if spec.target.family == "aarch64":
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makefile.filter("ppc64 ia64", "ppc64 ia64 aarch64")
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def build(self, spec, prefix):
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with working_dir(self.build_directory):
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make()
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make("127mer=1", parallel=False)
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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install("SOAPdenovo-Trans-*mer", prefix.bin)
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