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New package: r-codex (#14869)

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This PR adds the r-codex package.

- new package: r-bsgenome-hsapiens-ucsc-hg19
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Glenn Johnson 2020-02-13 20:00:39 -06:00 committed by GitHub
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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 RBsgenomeHsapiensUcscHg19(RPackage):
"""Full genome sequences for Homo sapiens (Human) as provided by UCSC
(hg19, Feb. 2009) and stored in Biostrings objects."""
# This is a bioconductor package but there is no available git repo.
homepage = "http://www.bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html"
url = "http://www.bioconductor.org/packages/release/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz"
version('1.4.0', sha256='88f515e5c27dd11d10654250e3a0a9389e4dfeb0b1c2d43419aa7086e6c516f8')
depends_on('r-bsgenome@1.33.5:', 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 RCodex(RPackage):
"""A normalization and copy number variation calling procedure for whole
exome DNA sequencing data. CODEX relies on the availability of multiple
samples processed using the same sequencing pipeline for normalization, and
does not require matched controls. The normalization model in CODEX
includes terms that specifically remove biases due to GC content, exon
length and targeting and amplification efficiency, and latent systemic
artifacts. CODEX also includes a Poisson likelihood-based recursive
segmentation procedure that explicitly models the count-based exome
sequencing data."""
homepage = "http://www.bioconductor.org/packages/release/bioc/html/CODEX.html"
git = "https://git.bioconductor.org/packages/CODEX"
version('1.18.0', commit='9a95cccc7ff3fe587636317e21e39a07dddf80bc')
depends_on('r@3.2.3:', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-bsgenome-hsapiens-ucsc-hg19', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))