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# Copyright 2013-2023 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 Xhmm(MakefilePackage):
"""The XHMM C++ software suite was written to
call copy number variation (CNV) from next-generation
sequencing projects, where exome capture was used
(or targeted sequencing, more generally)."""
homepage = "http://atgu.mgh.harvard.edu/xhmm/index.shtml"
git = "https://bitbucket.org/statgen/xhmm.git"
version("20160104", commit="cc14e528d90932f059ac4fe94e869e81221fd732")
depends_on("lapack")
def edit(self, spec, prefix):
filter_file("GCC", "CC", "sources/hmm++/config_rules.Makefile")
filter_file("GCC =gcc", "", "sources/hmm++/config_defs.Makefile")
def build(self, spec, prefix):
make("LAPACK_LIBS=%s" % "".join(spec["lapack"].libs.names))
def install(self, spec, prefix):
mkdir(prefix.bin)
install("xhmm", prefix.bin)
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