GNU bug report logs - #47490
[PATCH] r-txdb-dmelanogaster-ucsc-dm6-ensgene

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: "Hong.Li <at> mdc-berlin.de" <Hong.Li <at> mdc-berlin.de>
To: "guix-patches <at> gnu.org" <guix-patches <at> gnu.org>
Cc: "Ricardo.Wurmus <at> mdc-berlin.de" <Ricardo.Wurmus <at> mdc-berlin.de>
Subject: [PATCH] r-txdb-dmelanogaster-ucsc-dm6-ensgene
Date: Mon, 29 Mar 2021 23:00:44 +0000

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

From 2621d8b89a4406bce271436640b8b7fd7764b8c0 Mon Sep 17 00:00:00 2001
From: hli <hli <at> mdc-berlin.de>
Date: Tue, 30 Mar 2021 00:53:51 +0200
Subject: [PATCH] r-txdb-dmelanogaster-ucsc-dm6-ensgene

---
 gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0bcd9a67cd..a8601d7ed2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -619,6 +619,36 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
      "This package exposes an annotation database generated from Ensembl.")
     (license license:artistic2.0)))

+(define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
+  (package
+    (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene")
+    (version "3.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri
+             "TxDb.Dmelanogaster.UCSC.dm6.ensGene"
+             version
+             'annotation))
+       (sha256
+        (base32
+         "0yij7zyqkmmr13389rs2gfa5anvvw648nnl1kjbsgvyxkggif8q4"))))
+    (properties
+     `((upstream-name
+        .
+        "TxDb.Dmelanogaster.UCSC.dm6.ensGene")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-genomicfeatures" ,r-genomicfeatures)))
+    (home-page
+     "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene")
+    (synopsis
+     "Annotation package for TxDb object(s)")
+    (description
+     "Exposes an annotation databases generated from UCSC by exposing these as TxDb objects")
+    (license license:artistic2.0)))
+
 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
   (package
     (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
--
2.17.1

[Message part 2 (text/html, inline)]

Message #10 received at 47490-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: "Li, Hong" <Hong.Li <at> mdc-berlin.de>
Cc: 47490-done <at> debbugs.gnu.org
Subject: Re: [PATCH] r-txdb-dmelanogaster-ucsc-dm6-ensgene
Date: Mon, 12 Apr 2021 18:37:58 +0200

Li, Hong <Hong.Li <at> mdc-berlin.de> writes:

> From 2621d8b89a4406bce271436640b8b7fd7764b8c0 Mon Sep 17 00:00:00 2001
> From: hli <hli <at> mdc-berlin.de>
> Date: Tue, 30 Mar 2021 00:53:51 +0200
> Subject: [PATCH] r-txdb-dmelanogaster-ucsc-dm6-ensgene

Thank you, I pushed it with minor tweaks and a conventional commit
message with commit eb8da54170919bc31946f492da1071dd491e942a.

PS: you can generate a commit (or a series of commits) with the expected
commit message by running ./etc/committer.scm.

-- 
Ricardo

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