From 2acaaee55007ddae404661e9f260ca720cbcda2d Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 19 Oct 2016 09:55:45 +0200 Subject: gnu: Add r-getopt. * gnu/packages/bioinformatics.scm (r-getopt): New variable. --- gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 43faaa078f..a7e4d0990d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5888,6 +5888,28 @@ packages.") Bioconductor, CRAN, and Github.") (license license:artistic2.0))) +(define-public r-getopt + (package + (name "r-getopt") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "getopt" version)) + (sha256 + (base32 + "00f57vgnzmg7cz80rjmjz1556xqcmx8nhrlbbhaq4w7gl2ibl87r")))) + (build-system r-build-system) + (home-page "https://github.com/trevorld/getopt") + (synopsis "Command-line option processor for R") + (description + "This package is designed to be used with Rscript to write shebang +scripts that accept short and long options. Many users will prefer to +use the packages @code{optparse} or @code{argparse} which add extra +features like automatically generated help options and usage texts, +support for default values, positional argument support, etc.") + (license license:gpl2+))) + (define-public r-dnacopy (package (name "r-dnacopy") -- cgit 1.4.1 From c79ad57a8def00a3fbefc7cac1f2306aaa1056bd Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 19 Oct 2016 10:48:56 +0200 Subject: gnu: Add r-optparse. * gnu/packages/bioinformatics.scm (r-optparse): New variable. --- gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a7e4d0990d..00770e8fbb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5910,6 +5910,29 @@ features like automatically generated help options and usage texts, support for default values, positional argument support, etc.") (license license:gpl2+))) +(define-public r-optparse + (package + (name "r-optparse") + (version "1.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "optparse" version)) + (sha256 + (base32 + "1g8as89r91xxi5j5azsd6vrfrhg84mnfx2683j7pacdp8s33radw")))) + (build-system r-build-system) + (propagated-inputs + `(("r-getopt" ,r-getopt))) + (home-page + "https://github.com/trevorld/optparse") + (synopsis "Command line option parser") + (description + "This package provides a command line parser inspired by Python's +@code{optparse} library to be used with Rscript to write shebang scripts +that accept short and long options.") + (license license:gpl2+))) + (define-public r-dnacopy (package (name "r-dnacopy") -- cgit 1.4.1 From 207ce8fbe5a906789aafa4d337675c627ce592d8 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 19 Oct 2016 15:09:55 +0200 Subject: gnu: Add r-biocviews. * gnu/packages/bioinformatics.scm (r-biocviews): New variable. --- gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 00770e8fbb..d58227408c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5888,6 +5888,34 @@ packages.") Bioconductor, CRAN, and Github.") (license license:artistic2.0))) +(define-public r-biocviews + (package + (name "r-biocviews") + (version "1.42.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "biocViews" version)) + (sha256 + (base32 + "07rjk10b91pkriyq297w86199r2d3sfji3ggs9mq2gyalsa8y4b6")))) + (properties + `((upstream-name . "biocViews"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-graph" ,r-graph) + ("r-rbgl" ,r-rbgl) + ("r-rcurl" ,r-rcurl) + ("r-xml" ,r-xml) + ("r-knitr" ,r-knitr) + ("r-runit" ,r-runit))) + (home-page "http://bioconductor.org/packages/biocViews") + (synopsis "Bioconductor package categorization helper") + (description "The purpose of biocViews is to create HTML pages that +categorize packages in a Bioconductor package repository according to keywords, +also known as views, in a controlled vocabulary.") + (license license:artistic2.0))) + (define-public r-getopt (package (name "r-getopt") -- cgit 1.4.1 From 99df12cd1921dd497bb4fcdd96ee40e358d71e6d Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 19 Oct 2016 15:21:17 +0200 Subject: gnu: Add r-biocstyle. * gnu/packages/bioinformatics.scm (r-biocstyle): New variable. --- gnu/packages/bioinformatics.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d58227408c..3fe7b5f3ae 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5916,6 +5916,26 @@ categorize packages in a Bioconductor package repository according to keywords, also known as views, in a controlled vocabulary.") (license license:artistic2.0))) +(define-public r-biocstyle + (package + (name "r-biocstyle") + (version "2.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocStyle" version)) + (sha256 + (base32 + "0qbk23fz8cn260isd9xlh9lxfj4adar6iqzai01c4kz0p31f45za")))) + (properties + `((upstream-name . "BiocStyle"))) + (build-system r-build-system) + (home-page "http://bioconductor.org/packages/BiocStyle") + (synopsis "Bioconductor formatting styles") + (description "This package provides standard formatting styles for +Bioconductor PDF and HTML documents. Package vignettes illustrate use and +functionality.") + (license license:artistic2.0))) + (define-public r-getopt (package (name "r-getopt") -- cgit 1.4.1