50 lines
2.5 KiB
Python
50 lines
2.5 KiB
Python
# Copyright 2013-2023 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.package import *
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class RBiomartr(RPackage):
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"""Genomic Data Retrieval.
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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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cran = "biomartr"
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version("1.0.2", sha256="7fd6cccd915aa39e593fb7591107ab9792d98a119dd42f3f666e5184f4e42743")
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version("0.9.2", sha256="d88085696e9c5614828602254c33f2cdd3bbfeebc2f21a705eee3cb961097c89")
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depends_on("r@3.1.1:", type=("build", "run"), when="@1.0.2:")
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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"), when="@0.9.2:")
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depends_on("r-readr@1.4.0:", type=("build", "run"), when="@1.0.2:")
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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-withr", type=("build", "run"), when="@1.0.2:")
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depends_on("r-fs", type=("build", "run"))
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depends_on("r-fs@1.3.1:", type=("build", "run"), when="@0.9.2")
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