94c2e7e7b4
This PR adds 'http://' to the homepage setting of a few packages that do not have it set. Not having that set can cause problems with some wiki apps when embedding the homepage value into markdown syntax. - bowtie2 - exuberant-ctags - perl-want - samtools
66 lines
2.8 KiB
Python
66 lines
2.8 KiB
Python
# Copyright 2013-2020 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 = "http://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('1.10', sha256='7b9ec5f05d61ec17bd9a82927e45d8ef37f813f79eb03fe06c88377f1bd03585')
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version('1.9', sha256='083f688d7070082411c72c27372104ed472ed7a620591d06f928e653ebc23482')
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version('1.8', sha256='c942bc1d9b85fd1b05ea79c5afd2805d489cd36b2c2d8517462682a4d779be16')
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version('1.7', sha256='e7b09673176aa32937abd80f95f432809e722f141b5342186dfef6a53df64ca1')
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version('1.6', sha256='ee5cd2c8d158a5969a6db59195ff90923c662000816cc0c41a190b2964dbe49e')
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version('1.5', sha256='8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6')
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version('1.4', sha256='9aae5bf835274981ae22d385a390b875aef34db91e6355337ca8b4dd2960e3f4')
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version('1.3.1', sha256='6c3d74355e9cf2d9b2e1460273285d154107659efa36a155704b1e4358b7d67e')
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version('1.2', sha256='420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa')
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depends_on('zlib')
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depends_on('ncurses')
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depends_on('perl', type='run')
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depends_on('python', type='run')
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# htslib became standalone @1.3.1, must use corresponding version
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depends_on('htslib@1.10.2', when='@1.10')
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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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def install(self, spec, prefix):
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if '+termlib' in spec['ncurses']:
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curses_lib = '-lncursesw -ltinfow'
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else:
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curses_lib = '-lncursesw'
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if self.spec.version >= Version('1.3.1'):
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configure('--prefix={0}'.format(prefix),
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'--with-htslib={0}'.format(self.spec['htslib'].prefix),
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'--with-ncurses',
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'CURSES_LIB={0}'.format(curses_lib))
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make()
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make('install')
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else:
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make('prefix={0}'.format(prefix),
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'LIBCURSES={0}'.format(curses_lib))
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make('prefix={0}'.format(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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