############################################################################## # Copyright (c) 2013-2016, 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/llnl/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('1.4', '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@1.4", when='@1.4') depends_on("htslib@1.3.1", when='@1.3.1') depends_on('zlib', when='@1.2') # needed for builtin htslib 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")