36 lines
1.6 KiB
Python
36 lines
1.6 KiB
Python
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class RCodex(RPackage):
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"""A Normalization and Copy Number Variation Detection Method for Whole
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Exome Sequencing.
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A normalization and copy number variation calling procedure for whole
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exome DNA sequencing data. CODEX relies on the availability of multiple
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samples processed using the same sequencing pipeline for normalization, and
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does not require matched controls. The normalization model in CODEX
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includes terms that specifically remove biases due to GC content, exon
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length and targeting and amplification efficiency, and latent systemic
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artifacts. CODEX also includes a Poisson likelihood-based recursive
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segmentation procedure that explicitly models the count-based exome
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sequencing data."""
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bioc = "CODEX"
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version('1.26.0', commit='729fd10bd42d12edcedd65b5a8fb1579e5949718')
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version('1.22.0', commit='aa0ee4278111a46e0c790312b0526ba07aab22eb')
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version('1.18.0', commit='9a95cccc7ff3fe587636317e21e39a07dddf80bc')
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depends_on('r@3.2.3:', type=('build', 'run'))
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depends_on('r-rsamtools', type=('build', 'run'))
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depends_on('r-genomeinfodb', type=('build', 'run'))
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depends_on('r-bsgenome-hsapiens-ucsc-hg19', type=('build', 'run'))
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depends_on('r-iranges', type=('build', 'run'))
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depends_on('r-biostrings', type=('build', 'run'))
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depends_on('r-s4vectors', type=('build', 'run'))
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