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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 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):
copy('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)
install_tree('demo', prefix.doc)
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