cdaac58488
* add version 1.46.0 to bioconductor package r-a4 * add version 1.46.0 to bioconductor package r-a4base * add version 1.46.0 to bioconductor package r-a4classif * add version 1.46.0 to bioconductor package r-a4core * add version 1.46.0 to bioconductor package r-a4preproc * add version 1.46.0 to bioconductor package r-a4reporting * add version 1.52.0 to bioconductor package r-absseq * add version 1.28.0 to bioconductor package r-acde * add version 1.76.0 to bioconductor package r-acgh * add version 2.54.0 to bioconductor package r-acme * add version 1.68.0 to bioconductor package r-adsplit * add version 1.70.0 to bioconductor package r-affxparser * add version 1.76.0 to bioconductor package r-affy * add version 1.74.0 to bioconductor package r-affycomp * add version 1.58.0 to bioconductor package r-affycompatible * add version 1.56.0 to bioconductor package r-affycontam * add version 1.70.0 to bioconductor package r-affycoretools * add version 1.46.0 to bioconductor package r-affydata * add version 1.50.0 to bioconductor package r-affyilm * add version 1.68.0 to bioconductor package r-affyio * add version 1.74.0 to bioconductor package r-affyplm * add version 1.44.0 to bioconductor package r-affyrnadegradation * add version 1.46.0 to bioconductor package r-agdex * add version 3.30.0 to bioconductor package r-agilp * add version 2.48.0 to bioconductor package r-agimicrorna * add version 1.30.0 to bioconductor package r-aims * add version 1.30.0 to bioconductor package r-aldex2 * add version 1.36.0 to bioconductor package r-allelicimbalance * add version 1.24.0 to bioconductor package r-alpine * add version 2.60.0 to bioconductor package r-altcdfenvs * add version 2.22.0 to bioconductor package r-anaquin * add version 1.26.0 to bioconductor package r-aneufinder * add version 1.26.0 to bioconductor package r-aneufinderdata * add version 1.70.0 to bioconductor package r-annaffy * add version 1.76.0 to bioconductor package r-annotate * add version 1.60.0 to bioconductor package r-annotationdbi * add version 1.22.0 to bioconductor package r-annotationfilter * add version 1.40.0 to bioconductor package r-annotationforge * add version 3.6.0 to bioconductor package r-annotationhub * add version 3.28.0 to bioconductor package r-aroma-light * add version 1.30.0 to bioconductor package r-bamsignals * add version 2.14.0 to bioconductor package r-beachmat * add version 2.58.0 to bioconductor package r-biobase * add version 2.6.0 to bioconductor package r-biocfilecache * add version 0.44.0 to bioconductor package r-biocgenerics * add version 1.8.0 to bioconductor package r-biocio * add version 1.16.0 to bioconductor package r-biocneighbors * add version 1.32.1 to bioconductor package r-biocparallel * add version 1.14.0 to bioconductor package r-biocsingular * add version 2.26.0 to bioconductor package r-biocstyle * add version 3.16.0 to bioconductor package r-biocversion * add version 2.54.0 to bioconductor package r-biomart * add version 1.26.0 to bioconductor package r-biomformat * add version 2.66.0 to bioconductor package r-biostrings * add version 1.46.0 to bioconductor package r-biovizbase * add version 1.8.0 to bioconductor package r-bluster * add version 1.66.1 to bioconductor package r-bsgenome * add version 1.34.0 to bioconductor package r-bsseq * add version 1.40.0 to bioconductor package r-bumphunter * add version 2.64.0 to bioconductor package r-category * add version 2.28.0 to bioconductor package r-champ * add version 2.30.0 to bioconductor package r-champdata * add version 1.48.0 to bioconductor package r-chipseq * add version 4.6.0 to bioconductor package r-clusterprofiler * add version 1.34.0 to bioconductor package r-cner * add version 1.30.0 to bioconductor package r-codex * add version 2.14.0 to bioconductor package r-complexheatmap * add version 1.72.0 to bioconductor package r-ctc * add version 2.26.0 to bioconductor package r-decipher * add version 0.24.0 to bioconductor package r-delayedarray * add version 1.20.0 to bioconductor package r-delayedmatrixstats * add version 1.38.0 to bioconductor package r-deseq2 * add version 1.44.0 to bioconductor package r-dexseq * add version 1.40.0 to bioconductor package r-dirichletmultinomial * add version 2.12.0 to bioconductor package r-dmrcate * add version 1.72.0 to bioconductor package r-dnacopy * add version 3.24.1 to bioconductor package r-dose * add version 2.46.0 to bioconductor package r-dss * add version 3.40.0 to bioconductor package r-edger * add version 1.18.0 to bioconductor package r-enrichplot * add version 2.22.0 to bioconductor package r-ensembldb * add version 1.44.0 to bioconductor package r-exomecopy * add version 2.6.0 to bioconductor package r-experimenthub * add version 1.24.0 to bioconductor package r-fgsea * add version 2.70.0 to bioconductor package r-gcrma * add version 1.34.0 to bioconductor package r-gdsfmt * add version 1.80.0 to bioconductor package r-genefilter * add version 1.34.0 to bioconductor package r-genelendatabase * add version 1.70.0 to bioconductor package r-genemeta * add version 1.76.0 to bioconductor package r-geneplotter * add version 1.20.0 to bioconductor package r-genie3 * add version 1.34.3 to bioconductor package r-genomeinfodb * update r-genomeinfodbdata * add version 1.34.0 to bioconductor package r-genomicalignments * add version 1.50.2 to bioconductor package r-genomicfeatures * add version 1.50.1 to bioconductor package r-genomicranges * add version 2.66.0 to bioconductor package r-geoquery * add version 1.46.0 to bioconductor package r-ggbio * add version 3.6.2 to bioconductor package r-ggtree * add version 2.8.0 to bioconductor package r-glimma * add version 1.10.0 to bioconductor package r-glmgampoi * add version 5.52.0 to bioconductor package r-globaltest * update r-go-db * add version 1.18.0 to bioconductor package r-gofuncr * add version 2.24.0 to bioconductor package r-gosemsim * add version 1.50.0 to bioconductor package r-goseq * add version 2.64.0 to bioconductor package r-gostats * add version 1.76.0 to bioconductor package r-graph * add version 1.60.0 to bioconductor package r-gseabase * add version 1.30.0 to bioconductor package r-gtrellis * add version 1.42.0 to bioconductor package r-gviz * add version 1.26.0 to bioconductor package r-hdf5array * add version 1.70.0 to bioconductor package r-hypergraph * add version 1.34.0 to bioconductor package r-illumina450probevariants-db * add version 0.40.0 to bioconductor package r-illuminaio * add version 1.72.0 to bioconductor package r-impute * add version 1.36.0 to bioconductor package r-interactivedisplaybase * add version 2.32.0 to bioconductor package r-iranges * add version 1.58.0 to bioconductor package r-kegggraph * add version 1.38.0 to bioconductor package r-keggrest * add version 3.54.0 to bioconductor package r-limma * add version 2.50.0 to bioconductor package r-lumi * add version 1.74.0 to bioconductor package r-makecdfenv * add version 1.76.0 to bioconductor package r-marray * add version 1.10.0 to bioconductor package r-matrixgenerics * add version 1.6.0 to bioconductor package r-metapod * add version 2.44.0 to bioconductor package r-methylumi * add version 1.44.0 to bioconductor package r-minfi * add version 1.32.0 to bioconductor package r-missmethyl * add version 1.78.0 to bioconductor package r-mlinterfaces * add version 1.10.0 to bioconductor package r-mscoreutils * add version 2.24.0 to bioconductor package r-msnbase * add version 2.54.0 to bioconductor package r-multtest * add version 1.36.0 to bioconductor package r-mzid * add version 2.32.0 to bioconductor package r-mzr * add version 1.60.0 to bioconductor package r-oligoclasses * update r-org-hs-eg-db * add version 1.40.0 to bioconductor package r-organismdbi * add version 1.38.0 to bioconductor package r-pathview * add version 1.90.0 to bioconductor package r-pcamethods * update r-pfam-db * add version 1.42.0 to bioconductor package r-phyloseq * add version 1.60.0 to bioconductor package r-preprocesscore * add version 1.30.0 to bioconductor package r-protgenerics * add version 1.32.0 to bioconductor package r-quantro * add version 2.30.0 to bioconductor package r-qvalue * add version 1.74.0 to bioconductor package r-rbgl * add version 2.38.0 to bioconductor package r-reportingtools * add version 2.42.0 to bioconductor package r-rgraphviz * add version 2.42.0 to bioconductor package r-rhdf5 * add version 1.10.0 to bioconductor package r-rhdf5filters * add version 1.20.0 to bioconductor package r-rhdf5lib * add version 2.0.0 to bioconductor package r-rhtslib * add version 1.74.0 to bioconductor package r-roc * add version 1.26.0 to bioconductor package r-rots * add version 2.14.0 to bioconductor package r-rsamtools * add version 1.58.0 to bioconductor package r-rtracklayer * add version 0.36.0 to bioconductor package r-s4vectors * add version 1.6.0 to bioconductor package r-scaledmatrix * add version 1.26.0 to bioconductor package r-scater * add version 1.12.0 to bioconductor package r-scdblfinder * add version 1.26.0 to bioconductor package r-scran * add version 1.8.0 to bioconductor package r-scuttle * add version 1.64.0 to bioconductor package r-seqlogo * add version 1.56.0 to bioconductor package r-shortread * add version 1.72.0 to bioconductor package r-siggenes * add version 1.20.0 to bioconductor package r-singlecellexperiment * add version 1.32.0 to bioconductor package r-snprelate * add version 1.48.0 to bioconductor package r-snpstats * add version 2.34.0 to bioconductor package r-somaticsignatures * add version 1.10.0 to bioconductor package r-sparsematrixstats * add version 1.38.0 to bioconductor package r-spem * add version 1.36.0 to bioconductor package r-sseq * add version 1.28.0 to bioconductor package r-summarizedexperiment * add version 3.46.0 to bioconductor package r-sva * add version 1.36.0 to bioconductor package r-tfbstools * add version 1.20.0 to bioconductor package r-tmixclust * add version 2.50.0 to bioconductor package r-topgo * add version 1.22.0 to bioconductor package r-treeio * add version 1.26.0 to bioconductor package r-tximport * add version 1.26.0 to bioconductor package r-tximportdata * add version 1.44.0 to bioconductor package r-variantannotation * add version 3.66.0 to bioconductor package r-vsn * add version 2.4.0 to bioconductor package r-watermelon * add version 2.44.0 to bioconductor package r-xde * add version 1.56.0 to bioconductor package r-xmapbridge * add version 0.38.0 to bioconductor package r-xvector * add version 1.24.0 to bioconductor package r-yapsa * add version 1.24.0 to bioconductor package r-yarn * add version 1.44.0 to bioconductor package r-zlibbioc * make version resource consistent for r-bsgenome-hsapiens-ucsc-hg19 * make version resource consistent for r-go-db * make version resource consistent for r-kegg-db * make version resource consistent for r-org-hs-eg-db * make version resource consistent for r-pfam-db * new package: r-ggrastr * Patches not needed for new version * new package: r-hdo-db * new package: r-ggnewscale * new package: r-gson * Actually depends on ggplot2@3.4.0: * Fix formatting of r-hdo-db * Fix dependency version specifiers * Clean up duplicate dependency references
67 lines
3.6 KiB
Python
67 lines
3.6 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.package import *
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class RGgbio(RPackage):
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"""Visualization tools for genomic data.
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The ggbio package extends and specializes the grammar of graphics for
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biological data. The graphics are designed to answer common scientific
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questions, in particular those often asked of high throughput genomics
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data. All core Bioconductor data structures are supported, where
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appropriate. The package supports detailed views of particular genomic
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regions, as well as genome-wide overviews. Supported overviews include
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ideograms and grand linear views. High-level plots include sequence
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fragment length, edge-linked interval to data view, mismatch pileup, and
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several splicing summaries."""
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bioc = "ggbio"
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version("1.46.0", commit="d9c6cb495c7268bcaaab141231a9038aec8498bc")
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version("1.44.1", commit="0301d9464e304a8113ea4479185cd358855ca365")
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version("1.44.0", commit="cb21284a9803917fa76e116adfc456525c95f660")
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version("1.42.0", commit="3540047ef018957d59fba8af7d3c58e4659f8e26")
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version("1.38.0", commit="c39c51993f419cfc2f094e664477f25f5212a242")
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version("1.32.0", commit="04bd12fbe0b1c5c6b721a5f927e1352765f9bf88")
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version("1.30.0", commit="8b05258b089b06a743352e92058edda06c24cfb7")
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version("1.28.5", commit="594521ca556ef7d97cf4882ecfa54d22c2a2faba")
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version("1.26.1", commit="b4f4c898c92aa1082aa7574f1e5c2a0dae943fbc")
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version("1.24.1", commit="ef04c1bca1330f37152bcc21080cbde94849a094")
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depends_on("r-biocgenerics", type=("build", "run"))
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depends_on("r-ggplot2@1.0.0:", type=("build", "run"))
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depends_on("r-gridextra", type=("build", "run"))
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depends_on("r-scales", type=("build", "run"))
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depends_on("r-reshape2", type=("build", "run"))
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depends_on("r-gtable", type=("build", "run"))
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depends_on("r-hmisc", type=("build", "run"))
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depends_on("r-biovizbase@1.23.3:", type=("build", "run"))
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depends_on("r-biovizbase@1.28.2:", type=("build", "run"), when="@1.28.5:")
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depends_on("r-biovizbase@1.29.2:", type=("build", "run"), when="@1.30.0:")
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depends_on("r-biobase", type=("build", "run"))
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depends_on("r-s4vectors@0.13.13:", type=("build", "run"))
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depends_on("r-iranges", type=("build", "run"))
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depends_on("r-iranges@2.11.16:", type=("build", "run"), when="@1.26.1:")
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depends_on("r-genomeinfodb@1.1.3:", type=("build", "run"))
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depends_on("r-genomicranges@1.21.10:", type=("build", "run"))
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depends_on("r-genomicranges@1.29.14:", type=("build", "run"), when="@1.26.1:")
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depends_on("r-summarizedexperiment", type=("build", "run"))
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depends_on("r-biostrings", type=("build", "run"))
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depends_on("r-rsamtools@1.17.28:", type=("build", "run"))
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depends_on("r-genomicalignments@1.1.16:", type=("build", "run"))
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depends_on("r-bsgenome", type=("build", "run"))
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depends_on("r-variantannotation@1.11.4:", type=("build", "run"))
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depends_on("r-rtracklayer@1.25.16:", type=("build", "run"))
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depends_on("r-genomicfeatures@1.17.13:", type=("build", "run"))
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depends_on("r-genomicfeatures@1.29.11:", type=("build", "run"), when="@1.26.1:")
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depends_on("r-organismdbi", type=("build", "run"))
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depends_on("r-ggally", type=("build", "run"))
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depends_on("r-ensembldb@1.99.13:", type=("build", "run"))
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depends_on("r-annotationdbi", type=("build", "run"))
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depends_on("r-annotationfilter", type=("build", "run"))
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depends_on("r-rlang", type=("build", "run"), when="@1.28.5:")
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