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##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
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('1.6', '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@1.6', when='@1.6')
depends_on('htslib@1.4', when='@1.4')
depends_on('htslib@1.3.1', when='@1.3.1')
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")
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