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* add version 1.48.0 to bioconductor package r-a4 * add version 1.48.0 to bioconductor package r-a4base * add version 1.48.0 to bioconductor package r-a4classif * add version 1.48.0 to bioconductor package r-a4core * add version 1.48.0 to bioconductor package r-a4preproc * add version 1.48.0 to bioconductor package r-a4reporting * add version 1.54.0 to bioconductor package r-absseq * add version 1.30.0 to bioconductor package r-acde * add version 1.78.0 to bioconductor package r-acgh * add version 2.56.0 to bioconductor package r-acme * add version 1.70.0 to bioconductor package r-adsplit * add version 1.72.0 to bioconductor package r-affxparser * add version 1.78.0 to bioconductor package r-affy * add version 1.76.0 to bioconductor package r-affycomp * add version 1.58.0 to bioconductor package r-affycontam * add version 1.72.0 to bioconductor package r-affycoretools * add version 1.48.0 to bioconductor package r-affydata * add version 1.52.0 to bioconductor package r-affyilm * add version 1.70.0 to bioconductor package r-affyio * add version 1.76.0 to bioconductor package r-affyplm * add version 1.46.0 to bioconductor package r-affyrnadegradation * add version 1.48.0 to bioconductor package r-agdex * add version 3.32.0 to bioconductor package r-agilp * add version 2.50.0 to bioconductor package r-agimicrorna * add version 1.32.0 to bioconductor package r-aims * add version 1.32.0 to bioconductor package r-aldex2 * add version 1.38.0 to bioconductor package r-allelicimbalance * add version 1.26.0 to bioconductor package r-alpine * add version 2.62.0 to bioconductor package r-altcdfenvs * add version 2.24.0 to bioconductor package r-anaquin * add version 1.28.0 to bioconductor package r-aneufinder * add version 1.28.0 to bioconductor package r-aneufinderdata * add version 1.72.0 to bioconductor package r-annaffy * add version 1.78.0 to bioconductor package r-annotate * add version 1.62.0 to bioconductor package r-annotationdbi * add version 1.24.0 to bioconductor package r-annotationfilter * add version 1.42.0 to bioconductor package r-annotationforge * add version 3.8.0 to bioconductor package r-annotationhub * add version 3.30.0 to bioconductor package r-aroma-light * add version 1.32.0 to bioconductor package r-bamsignals * add version 2.16.0 to bioconductor package r-beachmat * add version 2.60.0 to bioconductor package r-biobase * add version 2.8.0 to bioconductor package r-biocfilecache * add version 0.46.0 to bioconductor package r-biocgeneric * add version 1.10.0 to bioconductor package r-biocio * add version 1.18.0 to bioconductor package r-biocneighbors * add version 1.34.0 to bioconductor package r-biocparallel * add version 1.16.0 to bioconductor package r-biocsingular * add version 2.28.0 to bioconductor package r-biocstyle * add version 3.17.1 to bioconductor package r-biocversion * add version 2.56.0 to bioconductor package r-biomart * add version 1.28.0 to bioconductor package r-biomformat * add version 2.68.0 to bioconductor package r-biostrings * add version 1.48.0 to bioconductor package r-biovizbase * add version 1.10.0 to bioconductor package r-bluster * add version 1.68.0 to bioconductor package r-bsgenome * add version 1.36.0 to bioconductor package r-bsseq * add version 1.42.0 to bioconductor package r-bumphunter * add version 2.66.0 to bioconductor package r-category * add version 2.30.0 to bioconductor package r-champ * add version 2.32.0 to bioconductor package r-champdata * add version 1.50.0 to bioconductor package r-chipseq * add version 4.8.0 to bioconductor package r-clusterprofiler * add version 1.36.0 to bioconductor package r-cner * add version 1.32.0 to bioconductor package r-codex * add version 2.16.0 to bioconductor package r-complexheatmap * add version 1.74.0 to bioconductor package r-ctc * add version 2.28.0 to bioconductor package r-decipher * add version 0.26.0 to bioconductor package r-delayedarray * add version 1.22.0 to bioconductor package r-delayedmatrixstats * add version 1.40.0 to bioconductor package r-deseq2 * add version 1.46.0 to bioconductor package r-dexseq * add version 1.42.0 to bioconductor package r-dirichletmultinomial * add version 2.14.0 to bioconductor package r-dmrcate * add version 1.74.0 to bioconductor package r-dnacopy * add version 3.26.0 to bioconductor package r-dose * add version 2.48.0 to bioconductor package r-dss * add version 3.42.0 to bioconductor package r-edger * add version 1.20.0 to bioconductor package r-enrichplot * add version 2.24.0 to bioconductor package r-ensembldb * add version 1.46.0 to bioconductor package r-exomecopy * add version 2.8.0 to bioconductor package r-experimenthub * add version 1.26.0 to bioconductor package r-fgsea * add version 2.72.0 to bioconductor package r-gcrma * add version 1.36.0 to bioconductor package r-gdsfmt * add version 1.82.0 to bioconductor package r-genefilter * add version 1.36.0 to bioconductor package r-genelendatabase * add version 1.72.0 to bioconductor package r-genemeta * add version 1.78.0 to bioconductor package r-geneplotter * add version 1.22.0 to bioconductor package r-genie3 * add version 1.36.0 to bioconductor package r-genomeinfodb * update r-genomeinfodbdata * add version 1.36.0 to bioconductor package r-genomicalignments * add version 1.52.0 to bioconductor package r-genomicfeatures * add version 1.52.0 to bioconductor package r-genomicranges * add version 2.68.0 to bioconductor package r-geoquery * add version 1.48.0 to bioconductor package r-ggbio * add version 3.8.0 to bioconductor package r-ggtree * add version 2.10.0 to bioconductor package r-glimma * add version 1.12.0 to bioconductor package r-glmgampoi * add version 5.54.0 to bioconductor package r-globaltest * update r-go-db * add version 1.20.0 to bioconductor package r-gofuncr * add version 2.26.0 to bioconductor package r-gosemsim * add version 1.52.0 to bioconductor package r-goseq * add version 2.66.0 to bioconductor package r-gostats * add version 1.78.0 to bioconductor package r-graph * add version 1.62.0 to bioconductor package r-gseabase * add version 1.32.0 to bioconductor package r-gtrellis * add version 1.44.0 to bioconductor package r-gviz * add version 1.28.0 to bioconductor package r-hdf5array * add version 1.72.0 to bioconductor package r-hypergraph * add version 1.36.0 to bioconductor package r-illumina450probevariants-db * add version 0.42.0 to bioconductor package r-illuminaio * add version 1.74.0 to bioconductor package r-impute * add version 1.38.0 to bioconductor package r-interactivedisplaybase * add version 2.34.0 to bioconductor package r-iranges * add version 1.60.0 to bioconductor package r-kegggraph * add version 1.40.0 to bioconductor package r-keggrest * add version 3.56.0 to bioconductor package r-limma * add version 2.52.0 to bioconductor package r-lumi * add version 1.76.0 to bioconductor package r-makecdfenv * add version 1.78.0 to bioconductor package r-marray * add version 1.12.0 to bioconductor package r-matrixgenerics * add version 1.8.0 to bioconductor package r-metapod * add version 2.46.0 to bioconductor package r-methylumi * add version 1.46.0 to bioconductor package r-minfi * add version 1.34.0 to bioconductor package r-missmethyl * add version 1.80.0 to bioconductor package r-mlinterfaces * add version 1.12.0 to bioconductor package r-mscoreutils * add version 2.26.0 to bioconductor package r-msnbase * add version 2.56.0 to bioconductor package r-multtest * add version 1.38.0 to bioconductor package r-mzid * add version 2.34.0 to bioconductor package r-mzr * add version 1.62.0 to bioconductor package r-oligoclasses * update r-org-hs-eg-db * add version 1.42.0 to bioconductor package r-organismdbi * add version 1.40.0 to bioconductor package r-pathview * add version 1.92.0 to bioconductor package r-pcamethods * update r-pfam-db * add version 1.44.0 to bioconductor package r-phyloseq * add version 1.62.0 to bioconductor package r-preprocesscore * add version 1.32.0 to bioconductor package r-protgenerics * add version 1.34.0 to bioconductor package r-quantro * add version 2.32.0 to bioconductor package r-qvalue * add version 1.76.0 to bioconductor package r-rbgl * add version 2.40.0 to bioconductor package r-reportingtools * add version 2.44.0 to bioconductor package r-rgraphviz * add version 2.44.0 to bioconductor package r-rhdf5 * add version 1.12.0 to bioconductor package r-rhdf5filters * add version 1.22.0 to bioconductor package r-rhdf5lib * add version 1.76.0 to bioconductor package r-roc * add version 1.28.0 to bioconductor package r-rots * add version 2.16.0 to bioconductor package r-rsamtools * add version 1.60.0 to bioconductor package r-rtracklayer * add version 0.38.0 to bioconductor package r-s4vectors * add version 1.8.0 to bioconductor package r-scaledmatrix * add version 1.28.0 to bioconductor package r-scater * add version 1.14.0 to bioconductor package r-scdblfinder * add version 1.28.0 to bioconductor package r-scran * add version 1.10.0 to bioconductor package r-scuttle * add version 1.66.0 to bioconductor package r-seqlogo * add version 1.58.0 to bioconductor package r-shortread * add version 1.74.0 to bioconductor package r-siggenes * add version 1.22.0 to bioconductor package r-singlecellexperiment * add version 1.34.0 to bioconductor package r-snprelate * add version 1.50.0 to bioconductor package r-snpstats * add version 2.36.0 to bioconductor package r-somaticsignatures * add version 1.12.0 to bioconductor package r-sparsematrixstats * add version 1.40.0 to bioconductor package r-spem * add version 1.38.0 to bioconductor package r-sseq * add version 1.30.0 to bioconductor package r-summarizedexperiment * add version 3.48.0 to bioconductor package r-sva * add version 1.38.0 to bioconductor package r-tfbstools * add version 1.22.0 to bioconductor package r-tmixclust * add version 2.52.0 to bioconductor package r-topgo * add version 1.24.0 to bioconductor package r-treeio * add version 1.28.0 to bioconductor package r-tximport * add version 1.28.0 to bioconductor package r-tximportdata * add version 1.46.0 to bioconductor package r-variantannotation * add version 3.68.0 to bioconductor package r-vsn * add version 2.6.0 to bioconductor package r-watermelon * add version 2.46.0 to bioconductor package r-xde * add version 1.58.0 to bioconductor package r-xmapbridge * add version 0.40.0 to bioconductor package r-xvector * add version 1.26.0 to bioconductor package r-yapsa * add version 1.26.0 to bioconductor package r-yarn * add version 1.46.0 to bioconductor package r-zlibbioc * Revert "add version 1.82.0 to bioconductor package r-genefilter" This reverts commit1702071c6d. * Revert "add version 0.38.0 to bioconductor package r-s4vectors" This reverts commit58a7df2387. * add version 0.38.0 to bioconductor package r-s4vectors * Revert "add version 1.28.0 to bioconductor package r-aneufinder" This reverts commit0a1f59de6c. * add version 1.28.0 to bioconductor package r-aneufinder * Revert "add version 2.16.0 to bioconductor package r-beachmat" This reverts commitcd49fb8e4c. * add version 2.16.0 to bioconductor package r-beachmat * Revert "add version 4.8.0 to bioconductor package r-clusterprofiler" This reverts commit6e9a951cbe. * add version 4.8.0 to bioconductor package r-clusterprofiler * Fix syntax error * r-genefilter: add version 1.82.0 * new package: r-basilisk-utils * new package: r-basilisk * new package: r-densvis * new package: r-dir-expiry * r-affyplm: add zlib dependency * r-cner: add zlib dependency * r-mzr: add zlib dependency * r-rhdf5filters: add zstd dependency * r-shortread: add zlib dependency * r-snpstats: add zlib dependency --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
72 lines
4.0 KiB
Python
72 lines
4.0 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 RVariantannotation(RPackage):
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"""Annotation of Genetic Variants.
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Annotate variants, compute amino acid coding changes, predict coding
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outcomes."""
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bioc = "VariantAnnotation"
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version("1.46.0", commit="80d43e024bead5afd48cb86910ba4670d8d37424")
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version("1.44.0", commit="2e7e0a3b7c1918c0d64170dc7c173a636d3764f4")
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version("1.42.1", commit="d1121696c76c189d6b4df9914806bf585a495845")
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version("1.40.0", commit="50ead7cb60cedf3c053853fab92d9f104f9f85bd")
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version("1.36.0", commit="9918bd19a2e6f89e5edc5fe03c8812f500bb3e19")
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version("1.30.1", commit="fb1ab00872570afb280522c4663e347dafc07a9e")
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version("1.28.13", commit="0393347b8ce2d5edf1a61589be93e6a93eda3419")
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version("1.26.1", commit="60ae67598cc3d7ed20ee6417920f8c209085faaf")
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version("1.24.5", commit="468d7f53fd743e04c9af853d58e871b4cc13a090")
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version("1.22.3", commit="3a91b6d4297aa416d5f056dec6f8925eb1a8eaee")
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depends_on("r@2.8.0:", type=("build", "run"))
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depends_on("r@4.0.0:", type=("build", "run"), when="@1.40.0:")
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depends_on("r-biocgenerics@0.15.3:", type=("build", "run"))
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depends_on("r-biocgenerics@0.37.0:", type=("build", "run"), when="@1.40.0:")
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depends_on("r-matrixgenerics", type=("build", "run"), when="@1.36.0:")
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depends_on("r-genomeinfodb@1.11.4:", type=("build", "run"))
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depends_on("r-genomeinfodb@1.15.2:", type=("build", "run"), when="@1.26.1:")
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depends_on("r-genomicranges@1.27.6:", type=("build", "run"))
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depends_on("r-genomicranges@1.31.8:", type=("build", "run"), when="@1.26.1:")
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depends_on("r-genomicranges@1.41.5:", type=("build", "run"), when="@1.36.0:")
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depends_on("r-summarizedexperiment@1.5.3:", type=("build", "run"))
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depends_on("r-summarizedexperiment@1.19.5:", type=("build", "run"), when="@1.36.0:")
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depends_on("r-rsamtools@1.23.10:", type=("build", "run"))
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depends_on("r-rsamtools@1.31.2:", type=("build", "run"), when="@1.26.1:")
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depends_on("r-rsamtools@1.33.6:", type=("build", "run"), when="@1.28.13:")
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depends_on("r-rsamtools@1.99.0:", type=("build", "run"), when="@1.30.1:")
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depends_on("r-dbi", type=("build", "run"))
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depends_on("r-zlibbioc", type=("build", "run"))
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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-s4vectors@0.17.24:", type=("build", "run"), when="@1.26.1:")
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depends_on("r-s4vectors@0.27.12:", type=("build", "run"), when="@1.36.0:")
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depends_on("r-iranges@2.3.25:", type=("build", "run"))
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depends_on("r-iranges@2.13.13:", type=("build", "run"), when="@1.26.1:")
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depends_on("r-iranges@2.23.9:", type=("build", "run"), when="@1.36.0:")
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depends_on("r-xvector@0.5.6:", type=("build", "run"))
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depends_on("r-xvector@0.19.7:", type=("build", "run"), when="@1.26.1:")
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depends_on("r-xvector@0.29.2:", type=("build", "run"), when="@1.36.0:")
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depends_on("r-biostrings@2.33.5:", type=("build", "run"))
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depends_on("r-biostrings@2.47.6:", type=("build", "run"), when="@1.26.1:")
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depends_on("r-biostrings@2.57.2:", type=("build", "run"), when="@1.36.0:")
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depends_on("r-annotationdbi@1.27.9:", type=("build", "run"))
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depends_on("r-rtracklayer@1.25.16:", type=("build", "run"))
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depends_on("r-rtracklayer@1.39.7:", type=("build", "run"), when="@1.26.1:")
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depends_on("r-bsgenome@1.37.6:", type=("build", "run"))
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depends_on("r-bsgenome@1.47.3:", type=("build", "run"), when="@1.26.1:")
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depends_on("r-genomicfeatures@1.27.4:", type=("build", "run"))
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depends_on("r-genomicfeatures@1.31.3:", type=("build", "run"), when="@1.26.1:")
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depends_on("r-rhtslib", type=("build", "run"), when="@1.30.1:")
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depends_on("r-rhtslib@1.99.3:", type=("build", "run"), when="@1.44.0:")
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depends_on("gmake", type="build")
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# Not listed but needed
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depends_on("curl")
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