From: Roel Janssen <roel@gnu.org>
To: Ricardo Wurmus <rekado@elephly.net>
Cc: 39201@debbugs.gnu.org
Subject: [bug#39201] [PATCH] gnu: Add r-deconstructsigs.
Date: Mon, 20 Jan 2020 20:32:56 +0100 [thread overview]
Message-ID: <cbbddcb542a05e4bab5b1d86ab7e1654bb1c2afa.camel@gnu.org> (raw)
In-Reply-To: <87h80qw9ml.fsf@elephly.net>
[-- Attachment #1: Type: text/plain, Size: 600 bytes --]
Hi Ricardo!
On Mon, 2020-01-20 at 14:16 +0100, Ricardo Wurmus wrote:
> Hi Roel,
>
> > 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?
>
> Please add the package to the bioconductor module instead and add a
> comment above to explain why. (That’s what we’ve done for other
> packages like this.)
So I did. Thanks for pointing this out.
I attached the new patch.
Thanks Ricardo!
Kind regards,
Roel Janssen
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[-- Type: text/x-patch, Size: 1946 bytes --]
From 403a80754c3f53c29c4430cc5a537ee781cc9b1e Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 20 Jan 2020 20:21:09 +0100
Subject: [PATCH] gnu: Add r-deconstructsigs.
* gnu/packages/bioconductor.scm (r-deconstructsigs): New variable.
---
gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ef34b99649..d4194e8ec2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -694,6 +694,34 @@ annotations.")
"This is a manifest package for Illumina's EPIC methylation arrays.")
(license license:artistic2.0)))
+;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
+;; from Bioconductor.
+(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-do-db
(package
(name "r-do-db")
--
2.25.0
next prev parent reply other threads:[~2020-01-20 19:34 UTC|newest]
Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-01-20 12:18 [bug#39201] [PATCH] gnu: Add r-deconstructsigs Roel Janssen
2020-01-20 13:16 ` Ricardo Wurmus
2020-01-20 19:32 ` Roel Janssen [this message]
2020-01-27 21:31 ` bug#39201: " Ricardo Wurmus
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