1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
|
# Copyright 2013-2022 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 *
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)
|
