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New package: r-exomedepth (#14884)

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This PR adds the r-exomedepth package and r-aod as a dependency.
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Glenn Johnson 2020-02-13 19:52:43 -06:00 committed by GitHub
parent 580c8f5b7e
commit 7996bc809a
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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 RAod(RPackage):
"""Provides a set of functions to analyse overdispersed counts or
proportions. Most of the methods are already available elsewhere but are
scattered in different packages. The proposed functions should be
considered as complements to more sophisticated methods such as generalized
estimating equations (GEE) or generalized linear mixed effect models
(GLMM)."""
homepage = "https://cloud.r-project.org/package=aod"
url = "https://cloud.r-project.org/src/contrib/aod_1.3.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/aod"
version('1.3.1', sha256='052d8802500fcfdb3b37a8e3e6f3fbd5c3a54e48c3f68122402d2ea3a15403bc')
depends_on('r@2.10:', type=('build', 'run'))

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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 RExomedepth(RPackage):
"""Calls copy number variants (CNVs) from targeted sequence data, typically
exome sequencing experiments designed to identify the genetic basis of
Mendelian disorders."""
homepage = "https://cloud.r-project.org/package=ExomeDepth"
url = "https://cloud.r-project.org/src/contrib/ExomeDepth_1.1.15.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ExomeDepth"
version('1.1.15', sha256='112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2')
depends_on('r@3.4.0:', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-genomicranges@1.23.0:', type=('build', 'run'))
depends_on('r-aod', type=('build', 'run'))
depends_on('r-vgam@0.8.4:', type=('build', 'run'))
depends_on('r-genomicalignments', type=('build', 'run'))
depends_on('r-dplyr', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))