49 lines
1.9 KiB
Python
49 lines
1.9 KiB
Python
# Copyright 2013-2022 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 glob
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import os.path
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from spack import *
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class Express(CMakePackage):
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"""eXpress is a streaming tool for quantifying the abundances of a set of
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target sequences from sampled subsequences."""
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homepage = "http://bio.math.berkeley.edu/eXpress/"
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url = "https://github.com/adarob/eXpress/archive/1.5.2.zip"
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# 1.5.1 used to be known as 2015-11-29 (same commit), but they've
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# added tags, so lets use 'em
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version('1.5.3', sha256='dfea819bbe7187a06462d6549a13f9cad7f3f128cb5c62bd90946f972c45a1f2')
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version('1.5.2', sha256='25a63cca3dac6bd0daf04d2f0b2275e47d2190c90522bd231b1d7a875a59a52e')
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version('1.5.1', sha256='fa3522de9cc25f1ede22fa196928912a6da2a2038681911115ec3e4da3d61293')
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depends_on('boost+date_time+exception+filesystem+system+chrono+atomic+container+math+thread+program_options')
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depends_on('bamtools')
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depends_on('zlib')
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# patch from the debian package repo:
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# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811859
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patch('gcc-6.patch', when='%gcc@6.0.0:')
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patch('gcc-6.patch', when='%fj')
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def patch(self):
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with working_dir('src'):
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files = glob.iglob('*.*')
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for file in files:
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if os.path.isfile(file):
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edit = FileFilter(file)
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edit.filter('#include <api', '#include <%s' % self.spec[
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'bamtools'].prefix.include.bamtools.api)
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edit = FileFilter('CMakeLists.txt')
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edit.filter(r'\${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/'
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'libbamtools.a', '%s' % self.spec['bamtools'].libs)
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def setup_build_environment(self, env):
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env.prepend_path('CPATH',
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self.spec['bamtools'].prefix.include.bamtools)
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