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# Copyright 2013-2024 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.package 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"
license("GPL-3.0-or-later")
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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