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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 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"
license("MIT")
version("1.0.7", sha256="03fa703873bdf9c32055c584448e1eece45f94b4bc68e60c9624cf3841e6d8a9")
version("1.0.5", sha256="386c6536bdaa4637579e235bac48444c08297337c490652d1e165accd34b258f")
depends_on("zlib-api", 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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