042fcc3575
* Add bioc attribute to r-do-db
* add version 1.38.1 to bioconductor package r-annotationforge
* add version 1.30.4 to bioconductor package r-biocparallel
* add version 2.64.1 to bioconductor package r-biostrings
* add version 4.4.4 to bioconductor package r-clusterprofiler
* add version 2.12.1 to bioconductor package r-complexheatmap
* add version 1.18.1 to bioconductor package r-delayedmatrixstats
* add version 3.22.1 to bioconductor package r-dose
* add version 3.38.4 to bioconductor package r-edger
* add version 1.16.2 to bioconductor package r-enrichplot
* add version 2.20.2 to bioconductor package r-ensembldb
* add version 1.32.4 to bioconductor package r-genomeinfodb
* add version 1.32.1 to bioconductor package r-genomicalignments
* add version 1.48.4 to bioconductor package r-genomicfeatures
* add version 1.44.1 to bioconductor package r-ggbio
* add version 3.4.4 to bioconductor package r-ggtree
* add version 1.24.2 to bioconductor package r-hdf5array
* add version 2.30.1 to bioconductor package r-iranges
* add version 1.36.3 to bioconductor package r-keggrest
* add version 3.52.4 to bioconductor package r-limma
* add version 1.8.1 to bioconductor package r-matrixgenerics
* update r-org-hs-eg-db
* add version 1.38.1 to bioconductor package r-organismdbi
* add version 1.36.1 to bioconductor package r-pathview
* add version 1.56.1 to bioconductor package r-rtracklayer
* add version 1.4.1 to bioconductor package r-scaledmatrix
* add version 1.24.1 to bioconductor package r-scran
* add version 1.6.3 to bioconductor package r-scuttle
* add version 1.18.1 to bioconductor package r-singlecellexperiment
* add version 1.20.2 to bioconductor package r-treeio
* Revert "Add bioc attribute to r-do-db"
This reverts commit 36be5c6072.
* Fix quotes on versions
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
59 lines
3.3 KiB
Python
59 lines
3.3 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 RRtracklayer(RPackage):
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"""R interface to genome annotation files and the UCSC genome browser.
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Extensible framework for interacting with multiple genome browsers
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(currently UCSC built-in) and manipulating annotation tracks in various
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formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
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built-in). The user may export/import tracks to/from the supported
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browsers, as well as query and modify the browser state, such as the
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current viewport."""
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bioc = "rtracklayer"
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version("1.56.1", commit="4c6d2201fcb102d471bd88f4f51cc34317669955")
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version("1.56.0", commit="1d70f7dc464ad87a1fde61588cd9ae0cb86b6e86")
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version("1.54.0", commit="04cdd75521a8364e67a49d7352500dd4a3e83c55")
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version("1.50.0", commit="d2e61f72ff5d5a94c2c487ba108a37f23bfcc1e6")
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version("1.44.4", commit="aec96e85daf53b5c5eb2e89250d2755352be4de3")
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version("1.42.2", commit="76702f671faea736807d54aeecfbadcd152d94c5")
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version("1.40.6", commit="ba9a6e711504a702147383bc7abfcc36eb304df7")
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version("1.38.3", commit="f20db703c09dc7e808c09e9b78c15aec9e546248")
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version("1.36.6", commit="8c0ac7230f94e0c5a981acbb178c8de70e968131")
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depends_on("r@3.3:", type=("build", "run"))
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depends_on("r-genomicranges@1.21.20:", type=("build", "run"))
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depends_on("r-genomicranges@1.37.2:", type=("build", "run"), when="@1.50.0:")
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depends_on("r-xml@1.98-0:", type=("build", "run"))
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depends_on("r-biocgenerics@0.13.8:", type=("build", "run"))
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depends_on("r-biocgenerics@0.25.1:", type=("build", "run"), when="@1.40.6:")
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depends_on("r-biocgenerics@0.35.3:", type=("build", "run"), when="@1.50.0:")
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depends_on("r-s4vectors@0.13.13:", type=("build", "run"))
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depends_on("r-s4vectors@0.17.25:", type=("build", "run"), when="@1.40.6:")
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depends_on("r-s4vectors@0.19.22:", type=("build", "run"), when="@1.42.2:")
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depends_on("r-s4vectors@0.23.18:", type=("build", "run"), when="@1.50.0:")
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depends_on("r-iranges@2.3.7:", type=("build", "run"))
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depends_on("r-iranges@2.11.12:", type=("build", "run"), when="@1.38.3:")
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depends_on("r-iranges@2.13.13:", type=("build", "run"), when="@1.40.6:")
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depends_on("r-xvector@0.9.4:", type=("build", "run"))
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depends_on("r-xvector@0.19.7:", type=("build", "run"), when="@1.40.6:")
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depends_on("r-genomeinfodb@1.3.14:", type=("build", "run"))
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depends_on("r-genomeinfodb@1.15.2:", type=("build", "run"), when="@1.40.6:")
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depends_on("r-biostrings@2.43.7:", type=("build", "run"))
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depends_on("r-biostrings@2.47.6:", type=("build", "run"), when="@1.40.6:")
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depends_on("r-zlibbioc", type=("build", "run"))
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depends_on("r-rcurl@1.4-2:", type=("build", "run"))
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depends_on("r-rsamtools@1.17.8:", type=("build", "run"))
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depends_on("r-rsamtools@1.31.2:", type=("build", "run"), when="@1.40.6:")
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depends_on("r-genomicalignments@1.5.4:", type=("build", "run"))
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depends_on("r-genomicalignments@1.15.6:", type=("build", "run"), when="@1.40.6:")
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depends_on("r-biocio", type=("build", "run"), when="@1.54.0:")
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depends_on("r-restfulr@0.0.13:", type=("build", "run"), when="@1.54.0:")
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