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# Copyright 2013-2022 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 = "https://gmt.genome.wustl.edu/packages/pindel/"
url = "https://github.com/genome/pindel/archive/v0.2.5.tar.gz"
version('0.2.5b8', sha256='7f21fda0b751d420831724d96e60873ce332139cfd24396e81c7f1ae2f707a19')
version('0.2.5b6', sha256='fe19aabdcf6334b9efe92d4509b80f0f266e621f1cc8db017b301d7e32e2eeac')
version('0.2.5b5', sha256='2ebe9d959d8c3862d9103d8a3768265dcc79eab547035857dca8ab8cfe2544e4')
version('0.2.5b4', sha256='0f6afd6b83f6cceb31be5dbb686c6ff518c54135274931097a8b83b3f5d0372a')
version('0.2.5b1', sha256='b626e23ddfb3590174cfe38458b537e96707eedc6c2b054504f72ca141ba306c')
version('0.2.5a7', sha256='0a270483dee9ef617d422eb61d3478334ee8f55e952d0a439529c2b21fcf8fb4')
version('0.2.5', sha256='9908940d090eff23d940c3b6f2f6b3fc2bb1fd3b7a2d553cc81eed240a23fd9f')
depends_on('htslib@1.7:')
# GCC > 4.8 seems to dislike calling abs on an unsigned integer
# replace ambiguous calls to abs() on the difference between two
# unsigned ints with a one line funtion that returns the 'absolute
# value' of the difference between two unsigned ints.
patch('gcc-5-compat.patch', when='@0.2.5b8%gcc@5:')
build_directory = 'src'
def edit(self, spec, prefix):
filter_file('include ../Makefile.local', '', 'src/Makefile')
filter_file('Makefile.local', '', 'src/Makefile')
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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