a8ccb8e116
- [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files
- [x] update all licensed files to say 2013-2021 using
`spack license update-copyright-year`
- [x] appease mypy with some additions to package.py that needed
for oneapi.py
45 lines
2.2 KiB
Python
45 lines
2.2 KiB
Python
# Copyright 2013-2021 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 RBiomartr(RPackage):
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"""Perform large scale genomic data retrieval and functional annotation
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retrieval. This package aims to provide users with a standardized way to
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automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and
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metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL',
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'ENSEMBLGENOMES', and 'UniProt' databases. Furthermore, an interface to the
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'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>)
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allows users to retrieve functional annotation for genomic loci. In
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addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt
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et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI
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Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. as well as
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'ENSEMBL' and 'ENSEMBLGENOMES' with only one command."""
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homepage = "https://docs.ropensci.org/biomartr"
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url = "https://cloud.r-project.org/src/contrib/biomartr_0.9.2.tar.gz"
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list_url = "https://cloud.r-project.org/src/contrib/Archive/biomartr"
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version('0.9.2', sha256='d88085696e9c5614828602254c33f2cdd3bbfeebc2f21a705eee3cb961097c89')
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depends_on('r-biomart', type=('build', 'run'))
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depends_on('r-biostrings', type=('build', 'run'))
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depends_on('r-curl', type=('build', 'run'))
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depends_on('r-tibble', type=('build', 'run'))
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depends_on('r-jsonlite', type=('build', 'run'))
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depends_on('r-data-table@1.9.4:', type=('build', 'run'))
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depends_on('r-dplyr@0.3.0:', type=('build', 'run'))
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depends_on('r-readr@0.2.2:', type=('build', 'run'))
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depends_on('r-downloader@0.3:', type=('build', 'run'))
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depends_on('r-rcurl@1.95-4.5:', type=('build', 'run'))
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depends_on('r-xml@3.98-1.1:', type=('build', 'run'))
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depends_on('r-httr@0.6.1:', type=('build', 'run'))
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depends_on('r-stringr@0.6.2:', type=('build', 'run'))
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depends_on('r-purrr', type=('build', 'run'))
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depends_on('r-r-utils', type=('build', 'run'))
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depends_on('r-philentropy', type=('build', 'run'))
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depends_on('r-fs@1.3.1:', type=('build', 'run'))
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