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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 *
from spack.pkg.builtin.boost import Boost
class RPhantompeakqualtools(RPackage):
"""Computes informative enrichment and quality measures for
ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. This is a modified version
of r-spp to be used in conjunction with the phantompeakqualtools
package."""
homepage = "https://github.com/kundajelab/phantompeakqualtools"
url = "https://github.com/kundajelab/phantompeakqualtools/raw/master/spp_1.14.tar.gz"
version("1.14", sha256="d03be6163e82aed72298e54a92c181570f9975a395f57a69b21ac02b1001520b")
depends_on("boost@1.41.0:")
# TODO: replace this with an explicit list of components of Boost,
# for instance depends_on('boost +filesystem')
# See https://github.com/spack/spack/pull/22303 for reference
depends_on(Boost.with_default_variants)
depends_on("r-catools", type=("build", "run"))
depends_on("r-snow", type=("build", "run"))
depends_on("r-snowfall", type=("build", "run"))
depends_on("r-bitops", type=("build", "run"))
depends_on("r-rsamtools", type=("build", "run"))
conflicts("%gcc@6:")
def setup_build_environment(self, env):
env.set("BOOST_ROOT", self.spec["boost"].prefix)
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