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##############################################################################
# Copyright (c) 2013-2018, 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 *
from shutil import copytree, copyfile
class Pindel(MakefilePackage):
"""Pindel can detect breakpoints from next-gen sequence data."""
homepage = "http://gmt.genome.wustl.edu/packages/pindel/"
url = "https://github.com/genome/pindel/archive/v0.2.5.tar.gz"
version('0.2.5b8', 'e6de2ffb38ba1cb89351cdccabe78cde')
version('0.2.5b6', 'dc2febb18c203f0ef1ba02b7b882e94b')
version('0.2.5b5', '73e964bc19de9ab9e6e8a316353e3184')
version('0.2.5b4', 'b4aefd538d9f62578f46440c4bce497e')
version('0.2.5b1', 'a8e53e8919aa29093db13fad5ede93a5')
version('0.2.5a7', '5fb2bac6108547b5d60c38fc66abdfc4')
version('0.2.5', 'd4568cbb83ec25ef9f9f6f058b30053e')
depends_on('htslib@1.7:')
#
# This Makefile2 stuff is due to the original installer,
# The author wants to run make twice, the first
# time generates a Makefile.local then returns "false"
# User is then suppose to run make again and the
# package will compile. This is an attempt to
# stay as close to the original installer as possible
#
def edit(self, spec, prefix):
makefile2 = join_path(self.build_directory, 'Makefile2')
copyfile(join_path(self.build_directory, 'Makefile'), makefile2)
myedit = FileFilter(makefile2)
myedit.filter('-include Makefile.local', '#removed include')
myedit.filter('@false', '#removed autofailure')
def build(self, spec, prefix):
make("Makefile.local", "-f",
"Makefile2",
"HTSLIB=%s" % spec['htslib'].prefix)
make("HTSLIB=%s" % spec['htslib'].prefix)
def install(self, spec, prefix):
mkdirp(prefix.bin)
install('src/pindel', prefix.bin)
install('src/pindel2vcf', prefix.bin)
install('src/sam2pindel', prefix.bin)
install('src/pindel2vcf4tcga', prefix.bin)
copytree(join_path(self.build_directory, 'demo'),
prefix.doc,
symlinks=True)
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