diff options
8 files changed, 135 insertions, 4 deletions
diff --git a/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py b/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py index d92d43d277..905eb44d64 100644 --- a/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py +++ b/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py @@ -15,7 +15,11 @@ class BioconductorDupradar(RPackage): bioc = "dupradar" - version("1.30.0", sha256="a299d7a4578047dfc19237e34255b0f50f70ce41d29762ef9f5a7741ba35aa3d") + version( + "1.30.0", + sha256="a299d7a4578047dfc19237e34255b0f50f70ce41d29762ef9f5a7741ba35aa3d", + deprecated=True, + ) depends_on("r-kernsmooth") depends_on("subread") diff --git a/var/spack/repos/builtin/packages/bioconductor-ebseq/package.py b/var/spack/repos/builtin/packages/bioconductor-ebseq/package.py index 9a14a95c92..2893d6bfdc 100644 --- a/var/spack/repos/builtin/packages/bioconductor-ebseq/package.py +++ b/var/spack/repos/builtin/packages/bioconductor-ebseq/package.py @@ -23,7 +23,11 @@ class BioconductorEbseq(RPackage): bioc = "ebseq" - version("1.40.0", sha256="a5d3a88743d61062c6d68a426b19c53a4afd2fa216abc884d42c187780994378") + version( + "1.40.0", + sha256="a5d3a88743d61062c6d68a426b19c53a4afd2fa216abc884d42c187780994378", + deprecated=True, + ) depends_on("r-blockmodeling") depends_on("r-gplots") diff --git a/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py b/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py index 657473676a..8785ae0835 100644 --- a/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py +++ b/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py @@ -17,4 +17,8 @@ class BioconductorRsubread(RPackage): depends_on("r-matrix") depends_on("zlib-api") - version("2.14.2", sha256="ac8be0fad0eb2743443e3a60a9a94eec78c746638aaccca70e7166d034dcebb5") + version( + "2.14.2", + sha256="ac8be0fad0eb2743443e3a60a9a94eec78c746638aaccca70e7166d034dcebb5", + deprecated=True, + ) diff --git a/var/spack/repos/builtin/packages/bioconductor-tximeta/package.py b/var/spack/repos/builtin/packages/bioconductor-tximeta/package.py index fd1206a2c0..01900bb5ab 100644 --- a/var/spack/repos/builtin/packages/bioconductor-tximeta/package.py +++ b/var/spack/repos/builtin/packages/bioconductor-tximeta/package.py @@ -19,7 +19,11 @@ class BioconductorTximeta(RPackage): bioc = "tximeta" - version("1.18.1", sha256="ee486fc4b2352e2998a3c0c2064449ebcf09b5815f982597ea58311dc8064408") + version( + "1.18.1", + sha256="ee486fc4b2352e2998a3c0c2064449ebcf09b5815f982597ea58311dc8064408", + deprecated=True, + ) depends_on("r", type=("build", "run")) depends_on("r-annotationdbi") diff --git a/var/spack/repos/builtin/packages/r-dupradar/package.py b/var/spack/repos/builtin/packages/r-dupradar/package.py new file mode 100644 index 0000000000..b86c04c021 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dupradar/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.package import * + + +class RDupradar(RPackage): + """Assessment of duplication rates in RNA-Seq datasets""" + + maintainers("pabloaledo") + + bioc = "dupRadar" + + version("1.32.0", commit="7e07fc3a3901f8cae0203759fc24dd7df430a07f") + version("1.30.3", commit="19e3b13a148c47e69686cd1e872182c564fd4dcd") + version("1.30.0", commit="3d53d2d2e0c404a25845d78b8df8fee3f6b34eb5") + + depends_on("r@3.2:", type=("build", "run")) + depends_on("r-kernsmooth", type=("build", "run")) + depends_on("r-rsubread", type=("build", "run")) + depends_on("subread", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-ebseq/package.py b/var/spack/repos/builtin/packages/r-ebseq/package.py new file mode 100644 index 0000000000..3fd13c18b7 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ebseq/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.package import * + + +class REbseq(RPackage): + """An R package for gene and isoform differential expression analysis of RNA-seq data. + + R/EBSeq is an R package for identifying genes and isoforms differentially + expressed (DE) across two or more biological conditions in an RNA-seq + experiment. Details can be found in Leng et al., 2013. It provides the syntax + required for identifying DE genes and isoforms in a two-group RNA-seq + experiment as well for identifying DE genes across more than two conditions + (the commands for identifying DE isoforms across more than two conditions + are the same as those required for gene-level analysis).""" + + maintainers("pabloaledo") + + bioc = "EBSeq" + + version("2.0.0", commit="f1d4e4419988ab98540739c9349559fd437cb59f") + version("1.40.0", commit="7d1d2a2b4ea0df8cddfb5e57d6431f3948c5c4ca") + + depends_on("r@3.0:", type=("build", "run")) + depends_on("r-bh", type=("build", "run")) + depends_on("r-blockmodeling", type=("build", "run")) + depends_on("r-gplots", type=("build", "run")) + depends_on("r-rcppeigen@0.3.2.9.0:", type=("build", "run")) + depends_on("r-rcpp@0.12.11:", type=("build", "run")) + depends_on("r-testthat", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-rsubread/package.py b/var/spack/repos/builtin/packages/r-rsubread/package.py new file mode 100644 index 0000000000..1def92a934 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rsubread/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.package import * + + +class RRsubread(RPackage): + """Mapping, quantification and variant analysis of sequencing data""" + + bioc = "Rsubread" + + version("2.16.0", commit="62b92c9ed3fc2be89ed9f29e3db1809d1e115dbc") + version("2.14.2", commit="863bd98c6523b888da59335a6acb516d2676d412") + + depends_on("r", type=("build", "run")) + depends_on("r-matrix", type=("build", "run")) + depends_on("r-r-utils", type=("build", "run")) + depends_on("zlib-api", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-tximeta/package.py b/var/spack/repos/builtin/packages/r-tximeta/package.py new file mode 100644 index 0000000000..ee12ed3f9a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-tximeta/package.py @@ -0,0 +1,39 @@ +# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.package import * + + +class RTximeta(RPackage): + """Transcript Quantification Import with Automatic Metadata + + Transcript quantification import from Salmon and alevin with automatic + attachment of transcript ranges and release information, and other associated + metadata. De novo transcriptomes can be linked to the appropriate sources with + linkedTxomes and shared for computational reproducibility.""" + + bioc = "tximeta" + + version("1.20.0", commit="c9cf6d6a80ca5129b91d723867aca0aec12e8299") + version("1.18.3", commit="3caed00397476cfe9c379f4bc5a361023fdd6ffa") + version("1.18.0", commit="8f87d53bbd6f2d97821dd8f7fdd54624928f862d") + + depends_on("r", type=("build", "run")) + depends_on("r-annotationdbi", type=("build", "run")) + depends_on("r-annotationhub", type=("build", "run")) + depends_on("r-biocfilecache", type=("build", "run")) + depends_on("r-biostrings", type=("build", "run")) + depends_on("r-ensembldb", type=("build", "run")) + depends_on("r-genomeinfodb", type=("build", "run")) + depends_on("r-genomicfeatures", type=("build", "run")) + depends_on("r-genomicranges", type=("build", "run")) + depends_on("r-iranges", type=("build", "run")) + depends_on("r-jsonlite", type=("build", "run")) + depends_on("r-matrix", type=("build", "run")) + depends_on("r-r-utils", type=("build", "run")) + depends_on("r-s4vectors", type=("build", "run")) + depends_on("r-summarizedexperiment", type=("build", "run")) + depends_on("r-tibble", type=("build", "run")) + depends_on("r-tximport", type=("build", "run")) |