Subject: bug#56039: closed (Re: [bug#56039] [PATCH] gnu: Add r-annmap.)

From: [email-masked] (GNU bug Tracking System)
Date: Fri, 01 Jul 2022 08:26:03 +0000

Your bug report

#56039: [PATCH] gnu: Add r-annmap.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to [email-masked].

-- 
56039: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=56039
GNU Bug Tracking System
Contact [email-masked] with problems

Subject: Re: [bug#56039] [PATCH] gnu: Add r-annmap.
From: Ricardo Wurmus <[email-masked]>
To: Mădălin Ionel Patrașcu<[email-masked]>
Cc: [email-masked]
Date: Fri, 01 Jul 2022 10:25:37 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

Mădălin Ionel Patrașcu <[email-masked]> 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

Subject: [PATCH] gnu: Add r-annmap.
From: Mădălin Ionel Patrașcu<[email-masked]>
To: <[email-masked]>
Date: Fri, 17 Jun 2022 16:05:58 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

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