From 66e35ce63b346f5f13b2d48a76bc0da14637c58c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 6 Mar 2019 21:16:33 +0100
Subject: gnu: r-txdb-hsapiens-ucsc-hg19-knowngene: Move to (gnu packages
 bioconductor).

* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): Move
from here...
* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): ...to
here.
---
 gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f3ea87cdb1..316be1ca42 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -224,6 +224,38 @@ based on mapping using Entrez Gene identifiers.")
 genomes and gene ID formats, largely based on the UCSC table browser.")
     (license license:lgpl2.0+)))
 
+(define-public r-txdb-hsapiens-ucsc-hg19-knowngene
+  (package
+    (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
+    (version "3.2.2")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/annotation/" instead of "bioc/".
+              (uri (string-append "https://bioconductor.org/packages/"
+                                  "release/data/annotation/src/contrib"
+                                  "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
+    (properties
+     `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
+    (build-system r-build-system)
+    ;; As this package provides little more than a very large data file it
+    ;; doesn't make sense to build substitutes.
+    (arguments `(#:substitutable? #f))
+    (propagated-inputs
+     `(("r-genomicfeatures" ,r-genomicfeatures)))
+    (home-page
+     "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
+    (synopsis "Annotation package for human genome in TxDb format")
+    (description
+     "This package provides an annotation database of Homo sapiens genome
+data.  It is derived from the UCSC hg19 genome and based on the \"knownGene\"
+track.  The database is exposed as a @code{TxDb} object.")
+    (license license:artistic2.0)))
+
 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
   (package
     (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
-- 
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