53 lines
2.1 KiB
Python
53 lines
2.1 KiB
Python
# Copyright 2013-2019 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 Samtools(Package):
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"""SAM Tools provide various utilities for manipulating alignments in
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the SAM format, including sorting, merging, indexing and generating
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alignments in a per-position format"""
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homepage = "www.htslib.org"
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url = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2"
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version('1.9', 'cca9a40d9b91b007af2ff905cb8b5924')
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version('1.8', 'c6e981c92ca00a44656a708c4b52aba3')
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version('1.7', '2240175242b5183bfa6baf1483f68023')
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version('1.6', 'b756f05fd5d1a7042074417edb8c9aea')
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version('1.5', sha256='8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6')
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version('1.4', '8cbd7d2a0ec16d834babcd6c6d85d691')
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version('1.3.1', 'a7471aa5a1eb7fc9cc4c6491d73c2d88')
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version('1.2', '988ec4c3058a6ceda36503eebecd4122')
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depends_on('ncurses')
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# htslib became standalone @1.3.1, must use corresponding version
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depends_on('htslib@1.9', when='@1.9')
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depends_on('htslib@1.8', when='@1.8')
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depends_on('htslib@1.7', when='@1.7')
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depends_on('htslib@1.6', when='@1.6')
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depends_on('htslib@1.5', when='@1.5')
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depends_on('htslib@1.4', when='@1.4')
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depends_on('htslib@1.3.1', when='@1.3.1')
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depends_on('zlib')
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depends_on('bzip2')
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def install(self, spec, prefix):
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if self.spec.version >= Version('1.3.1'):
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configure('--prefix={0}'.format(prefix), '--with-ncurses',
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'CURSES_LIB=-lncursesw')
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make()
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make('install')
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else:
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make("prefix=%s" % prefix)
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make("prefix=%s" % prefix, "install")
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# Install dev headers and libs for legacy apps depending on them
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mkdir(prefix.include)
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mkdir(prefix.lib)
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install('sam.h', prefix.include)
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install('bam.h', prefix.include)
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install('libbam.a', prefix.lib)
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