* [bug#30984] [PATCH] gnu: Add r-regioner.
@ 2018-03-29 12:23 Roel Janssen
2018-03-30 14:49 ` bug#30984: " Leo Famulari
0 siblings, 1 reply; 2+ messages in thread
From: Roel Janssen @ 2018-03-29 12:23 UTC (permalink / raw)
To: 30984
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From b6b0a7900a3d8b87efe798ff65387838b7e2487c Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 29 Mar 2018 14:20:20 +0200
Subject: [PATCH] gnu: Add r-regioner.
* gnu/packages/bioconductor.scm (r-regioner): New variable.
---
gnu/packages/bioconductor.scm | 32 +++++++++++++++++++++++++++++++-
1 file changed, 31 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f557dce8e..09581d9fd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018 Roel Janssen <roel@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -21,7 +22,9 @@
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix build-system r)
- #:use-module (gnu packages))
+ #:use-module (gnu packages)
+ #:use-module (gnu packages statistics)
+ #:use-module (gnu packages bioinformatics))
(define-public r-hpar
(package
@@ -40,3 +43,30 @@
(description "This package provides a simple interface to and data from
the Human Protein Atlas project.")
(license license:artistic2.0)))
+
+(define-public r-regioner
+ (package
+ (name "r-regioner")
+ (version "1.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "regioneR" version))
+ (sha256
+ (base32
+ "1vprp3l929hwzmvgskbhawfgnrymwc9n2rxd16rgagnv1dxnjxfp"))))
+ (properties `((upstream-name . "regioneR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-memoise" ,r-memoise)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-iranges" ,r-iranges)))
+ (home-page "https://bioconductor.org/packages/regioneR/")
+ (synopsis "Association analysis of genomic regions")
+ (description "This package offers a statistical framework based on
+customizable permutation tests to assess the association between genomic
+region sets and other genomic features.")
+ (license license:artistic2.0)))
--
2.16.2
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Dear Guix,
I'd like to add “r-regioner”, which is a Bioconductor package. I
noticed there is a “bioconductor.scm” module. Should I add it there, or
should I add it to “bioinformatics.scm” instead?
Kind regards,
Roel Janssen
^ permalink raw reply related [flat|nested] 2+ messages in thread
* bug#30984: [PATCH] gnu: Add r-regioner.
2018-03-29 12:23 [bug#30984] [PATCH] gnu: Add r-regioner Roel Janssen
@ 2018-03-30 14:49 ` Leo Famulari
0 siblings, 0 replies; 2+ messages in thread
From: Leo Famulari @ 2018-03-30 14:49 UTC (permalink / raw)
To: Roel Janssen; +Cc: 30984-done
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On Thu, Mar 29, 2018 at 02:23:15PM +0200, Roel Janssen wrote:
> From b6b0a7900a3d8b87efe798ff65387838b7e2487c Mon Sep 17 00:00:00 2001
> From: Roel Janssen <roel@gnu.org>
> Date: Thu, 29 Mar 2018 14:20:20 +0200
> Subject: [PATCH] gnu: Add r-regioner.
>
> * gnu/packages/bioconductor.scm (r-regioner): New variable.
Thanks! Pushed as 183ce9884924794677eefca78cf445ada5551260
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