From ff4834c065a3b0d90021fbbba2f8306ade9ce691 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 3 Dec 2020 14:33:05 +0100 Subject: [PATCH] gnu: Add r-biocio. * gnu/packages/bioconductor.scm (r-biocio): New variable. --- gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6adce2500b..a854fef82e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8867,3 +8867,39 @@ etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as well as misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.") (license license:artistic2.0))) + +(define-public r-biocio + (package + (name "r-biocio") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocIO" version)) + (sha256 + (base32 + "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18")))) + (properties `((upstream-name . "BiocIO"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-rcurl" ,r-rcurl) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/BiocIO") + (synopsis "Standard input and output for Bioconductor packages") + (description + "This package implements `import()` and `export()` standard generics for +importing and exporting biological data formats. `import()` supports +whole-file as well as chunk-wise iterative import. The `import()` interface +optionally provides a standard mechanism for 'lazy' access via `filter()` (on +row or element-like components of the file resource), `select()` (on +column-like components of the file resource) and `collect()`. The `import()` +interface optionally provides transparent access to remote (e.g. via https) +as well as local access. Developers can register a file extension, e.g., +`.loom` for dispatch from character-based URIs to specific `import()` / +`export()` methods based on classes representing file types, e.g., +`LoomFile()`.") + (license license:artistic2.0))) -- 2.20.1