37 lines
1.4 KiB
Python
37 lines
1.4 KiB
Python
# Copyright 2013-2021 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 import *
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class Tophat(AutotoolsPackage):
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"""Spliced read mapper for RNA-Seq."""
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homepage = "http://ccb.jhu.edu/software/tophat/index.shtml"
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url = "https://github.com/infphilo/tophat/archive/v2.1.1.tar.gz"
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version('2.1.2', sha256='15016b82255dad085d4ee7d970e50f0e53a280d466335553d47790d8344ff4b1')
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version('2.1.1', sha256='991b1b7c840a5f5c4e9a15b2815983257d2b0748246af0b9094c7d07552b023e')
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depends_on('autoconf', type='build')
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# 2.1.1 only builds with automake@1.15.1. There's a patch here:
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# https://github.com/spack/spack/pull/8244, which was incorporated
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# upstream in 2.1.2, which is known to build with 1.16.1 and 1.15.1.
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depends_on('automake', type='build')
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depends_on('automake@1.15.1', when='@:2.1.1', type='build')
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depends_on('libtool', type='build')
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depends_on('m4', type='build')
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depends_on('boost@1.47:')
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depends_on('bowtie2', type='run')
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parallel = False
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def setup_build_environment(self, env):
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env.append_flags("CFLAGS", self.compiler.cxx98_flag)
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def configure_args(self):
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return ["--with-boost={0}".format(self.spec['boost'].prefix)]
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