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02/03: gnu: Add r-universalmotif.
From: |
guix-commits |
Subject: |
02/03: gnu: Add r-universalmotif. |
Date: |
Fri, 5 Mar 2021 10:07:41 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 1353e536054c3f7375d784885014add9b9ea990b
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Fri Mar 5 02:20:38 2021 +0100
gnu: Add r-universalmotif.
* gnu/packages/bioconductor.scm (r-universalmotif): New variable.
---
gnu/packages/bioconductor.scm | 52 ++++++++++++++++++++++++++++++++++++++++++-
1 file changed, 51 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a4d97fa..9e426df 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4,7 +4,7 @@
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019, 2020 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
-;;; Copyright © 2020 Mădălin Ionel Patrașcu
<madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu
<madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;;
;;; This file is part of GNU Guix.
@@ -7435,6 +7435,56 @@ data. This modified test allows for testing
differential expression in qPCR
data.")
(license license:gpl2+)))
+(define-public r-universalmotif
+ (package
+ (name "r-universalmotif")
+ (version "1.8.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "universalmotif" version))
+ (sha256
+ (base32
+ "1ys2kbayc1rzv8nzi60208yfslm4kzynndfg7vw2n0c30dvzycrc"))))
+ (properties
+ `((upstream-name . "universalmotif")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-reference-to-strip
+ (lambda _
+ (substitute* "src/Makevars"
+ (("/usr/bin/strip") (which "strip"))))))))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggseqlogo" ,r-ggseqlogo)
+ ("r-iranges" ,r-iranges)
+ ("r-mass" ,r-mass)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppthread" ,r-rcppthread)
+ ("r-rdpack" ,r-rdpack)
+ ("r-rlang" ,r-rlang)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-yaml" ,r-yaml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page
+ "https://bioconductor.org/packages/universalmotif/")
+ (synopsis
+ "Specific structures importer, modifier, and exporter for R")
+ (description
+ "This package allows importing most common @dfn{specific structure}
+(motif) types into R for use by functions provided by other Bioconductor
+motif-related packages. Motifs can be exported into most major motif formats
+from various classes as defined by other Bioconductor packages. A suite of
+motif and sequence manipulation and analysis functions are included, including
+enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
+motifs, and others.")
+ (license license:gpl3)))
+
;; This is a CRAN package, but it depends on Bioconductor packages, so we put
;; it here.
(define-public r-activedriverwgs