From: Roel Janssen <roel@gnu.org>
To: 39201@debbugs.gnu.org
Subject: [bug#39201] [PATCH] gnu: Add r-deconstructsigs.
Date: Mon, 20 Jan 2020 13:18:30 +0100 [thread overview]
Message-ID: <5d8aa06a6dd9845acfab5685b4106e7c382a7887.camel@gnu.org> (raw)
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Dear Guix,
Here's a patch to add r-deconstructsigs. I added it to the cran module
because that's where it originates from, but it takes a reference
genome from bioconductor. So I had to use the bioconductor module. Is
that OK?
Thanks for your hard work and valuable time.
Kind regards,
Roel Janssen
[-- Attachment #2: 0001-gnu-Add-r-deconstructsigs.patch --]
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From e2a436698e81ce6b70be982a2193e6307606be41 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 20 Jan 2020 13:14:52 +0100
Subject: [PATCH] gnu: Add r-deconstructsigs.
* gnu/packages/cran.scm (r-deconstructsigs): New variable.
---
gnu/packages/cran.scm | 29 ++++++++++++++++++++++++++++-
1 file changed, 28 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ff2490bc31..f4ecb9dec7 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2,7 +2,7 @@
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
-;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
@@ -43,6 +43,7 @@
#:use-module (guix build-system r)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
+ #:use-module (gnu packages bioconductor)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages c)
#:use-module (gnu packages compression)
@@ -1911,6 +1912,32 @@ instructed to explore various modifications of the objects (e.g., sorting
rows, dropping names) to see if the modified versions are identical.")
(license license:gpl2+)))
+(define-public r-deconstructsigs
+ (package
+ (name "r-deconstructsigs")
+ (version "1.8.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "deconstructSigs" version))
+ (sha256
+ (base32
+ "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
+ (properties
+ `((upstream-name . "deconstructSigs")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)
+ ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-reshape2" ,r-reshape2)))
+ (home-page "https://github.com/raerose01/deconstructSigs")
+ (synopsis "Identifies signatures present in a tumor sample")
+ (description "This package takes sample information in the form of the
+fraction of mutations in each of 96 trinucleotide contexts and identifies
+the weighted combination of published signatures that, when summed, most
+closely reconstructs the mutational profile.")
+ (license license:gpl2+)))
+
(define-public r-dendextend
(package
(name "r-dendextend")
--
2.17.1
next reply other threads:[~2020-01-20 12:19 UTC|newest]
Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-01-20 12:18 Roel Janssen [this message]
2020-01-20 13:16 ` [bug#39201] [PATCH] gnu: Add r-deconstructsigs Ricardo Wurmus
2020-01-20 19:32 ` Roel Janssen
2020-01-27 21:31 ` bug#39201: " Ricardo Wurmus
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