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# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Samtools(Package):
"""SAM Tools provide various utilities for manipulating alignments in
the SAM format, including sorting, merging, indexing and generating
alignments in a per-position format"""
homepage = "http://www.htslib.org"
url = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2"
version('1.12', sha256='6da3770563b1c545ca8bdf78cf535e6d1753d6383983c7929245d5dba2902dcb')
version('1.10', sha256='7b9ec5f05d61ec17bd9a82927e45d8ef37f813f79eb03fe06c88377f1bd03585')
version('1.9', sha256='083f688d7070082411c72c27372104ed472ed7a620591d06f928e653ebc23482')
version('1.8', sha256='c942bc1d9b85fd1b05ea79c5afd2805d489cd36b2c2d8517462682a4d779be16')
version('1.7', sha256='e7b09673176aa32937abd80f95f432809e722f141b5342186dfef6a53df64ca1')
version('1.6', sha256='ee5cd2c8d158a5969a6db59195ff90923c662000816cc0c41a190b2964dbe49e')
version('1.5', sha256='8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6')
version('1.4', sha256='9aae5bf835274981ae22d385a390b875aef34db91e6355337ca8b4dd2960e3f4')
version('1.3.1', sha256='6c3d74355e9cf2d9b2e1460273285d154107659efa36a155704b1e4358b7d67e')
version('1.2', sha256='420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa')
version('0.1.8', sha256='343daf96f035c499c5b82dce7b4d96b10473308277e40c435942b6449853815b',
url="https://github.com/samtools/samtools/archive/0.1.8.tar.gz")
depends_on('zlib')
depends_on('ncurses')
depends_on('perl', type='run')
depends_on('python', type='run')
# htslib became standalone @1.3.1, must use corresponding version
depends_on('htslib@1.13', when='@1.13')
depends_on('htslib@1.12', when='@1.12')
depends_on('htslib@1.11', when='@1.11')
depends_on('htslib@1.10.2', when='@1.10')
depends_on('htslib@1.9', when='@1.9')
depends_on('htslib@1.8', when='@1.8')
depends_on('htslib@1.7', when='@1.7')
depends_on('htslib@1.6', when='@1.6')
depends_on('htslib@1.5', when='@1.5')
depends_on('htslib@1.4', when='@1.4')
depends_on('htslib@1.3.1', when='@1.3.1')
def install(self, spec, prefix):
if '+termlib' in spec['ncurses']:
curses_lib = '-lncursesw -ltinfow'
else:
curses_lib = '-lncursesw'
if self.spec.version >= Version('1.3.1'):
configure('--prefix={0}'.format(prefix),
'--with-htslib={0}'.format(self.spec['htslib'].prefix),
'--with-ncurses',
'CURSES_LIB={0}'.format(curses_lib))
make()
make('install')
else:
make('prefix={0}'.format(prefix),
'LIBCURSES={0}'.format(curses_lib))
if self.spec.version == Version('0.1.8'):
make('prefix={0}'.format(prefix))
else:
make('prefix={0}'.format(prefix), 'install')
# Install dev headers and libs for legacy apps depending on them
mkdir(prefix.include)
mkdir(prefix.lib)
install('sam.h', prefix.include)
install('bam.h', prefix.include)
install('libbam.a', prefix.lib)
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