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# Copyright 2013-2020 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 Sniffles(CMakePackage):
"""Structural variation caller using third generation sequencing."""
homepage = "https://github.com/fritzsedlazeck/Sniffles/wiki"
url = "https://github.com/fritzsedlazeck/Sniffles/archive/v1.0.5.tar.gz"
version('1.0.7', sha256='03fa703873bdf9c32055c584448e1eece45f94b4bc68e60c9624cf3841e6d8a9')
version('1.0.5', sha256='386c6536bdaa4637579e235bac48444c08297337c490652d1e165accd34b258f')
depends_on('zlib', type='link')
depends_on('bamtools', type='link')
patch('unused_libs.patch')
def cmake_args(self):
i = self.spec['bamtools'].prefix.include.bamtools
return ['-DCMAKE_CXX_FLAGS=-I{0}'.format(i)]
# the build process doesn't actually install anything, do it by hand
def install(self, spec, prefix):
mkdir(prefix.bin)
src = "bin/sniffles-core-{0}".format(spec.version.dotted)
binaries = ['sniffles', 'sniffles-debug']
for b in binaries:
install(join_path(src, b), join_path(prefix.bin, b))
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