GNU bug report logs - #56039
[PATCH] gnu: Add r-annmap.

Previous Next

Full log

View this message in rfc822 format

From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#56039: closed ([PATCH] gnu: Add r-annmap.)
Date: Fri, 01 Jul 2022 08:26:03 +0000

[Message part 1 (text/plain, inline)]

Your message dated Fri, 01 Jul 2022 10:25:37 +0200
with message-id <871qv58cj4.fsf <at> elephly.net>
and subject line Re: [bug#56039] [PATCH] gnu: Add r-annmap.
has caused the debbugs.gnu.org bug report #56039,
regarding [PATCH] gnu: Add r-annmap.
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


-- 
56039: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=56039
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

[Message part 2 (message/rfc822, inline)]

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-annmap.
Date: Fri, 17 Jun 2022 16:05:58 +0200

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1e87b190c2..5b74118974 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2029,6 +2029,40 @@ (define-public r-aneufinder
 sequencing data.")
     (license license:artistic2.0)))
 
+(define-public r-annmap
+  (package
+    (name "r-annmap")
+    (version "1.38.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "annmap" version))
+              (sha256
+               (base32
+                "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv"))))
+    (properties `((upstream-name . "annmap")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biobase
+           r-biocgenerics
+           r-dbi
+           r-digest
+           r-genefilter
+           r-genomicranges
+           r-iranges
+           r-lattice
+           r-rmysql
+           r-rsamtools))
+    (home-page "https://github.com/cruk-mi/annmap")
+    (synopsis
+     "Genome annotation and visualisation for Affymetrix arrays and NGS analysis")
+    (description
+     "This package @code{annmap} provides annotation mappings for Affymetrix exon
+arrays and coordinate based queries to support deep sequencing data analysis.
+Database access is hidden behind the API which provides a set of functions such
+as @code{genesInRange()}, @code{geneToExon()}, @code{exonDetails()}, etc.
+Functions to plot gene architecture and BAM file data are also provided.")
+    (license license:gpl2)))
+
 (define-public r-biocversion
   (package
     (name "r-biocversion")

base-commit: d6bd483cd53cedc8da39fcc6c419f7241080ed21
-- 
2.36.1

[Message part 3 (message/rfc822, inline)]

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 56039-done <at> debbugs.gnu.org
Subject: Re: [bug#56039] [PATCH] gnu: Add r-annmap.
Date: Fri, 01 Jul 2022 10:25:37 +0200

Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> writes:

> diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
> index 1e87b190c2..5b74118974 100644
> --- a/gnu/packages/bioconductor.scm
> +++ b/gnu/packages/bioconductor.scm
> @@ -2029,6 +2029,40 @@ (define-public r-aneufinder
>  sequencing data.")
>      (license license:artistic2.0)))
>  
> +(define-public r-annmap

Thanks.  I applied it with a commit message.

-- 
Ricardo

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.