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# Copyright 2013-2018 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 = "www.htslib.org"
url = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2"
version('1.9', 'cca9a40d9b91b007af2ff905cb8b5924')
version('1.8', 'c6e981c92ca00a44656a708c4b52aba3')
version('1.7', '2240175242b5183bfa6baf1483f68023')
version('1.6', 'b756f05fd5d1a7042074417edb8c9aea')
version('1.4', '8cbd7d2a0ec16d834babcd6c6d85d691')
version('1.3.1', 'a7471aa5a1eb7fc9cc4c6491d73c2d88')
version('1.2', '988ec4c3058a6ceda36503eebecd4122')
depends_on('ncurses')
# htslib became standalone @1.3.1, must use corresponding version
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@1.4', when='@1.4')
depends_on('htslib@1.3.1', when='@1.3.1')
depends_on('zlib', when='@1.7:')
depends_on('bzip2', when='@1.7:')
def install(self, spec, prefix):
if self.spec.version >= Version('1.3.1'):
configure('--prefix={0}'.format(prefix), '--with-ncurses',
'CURSES_LIB=-lncursesw')
make()
make('install')
else:
make("prefix=%s" % prefix)
make("prefix=%s" % 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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