From aa30ab5aeebc14376ccc29a68d8b4e4fb8184fca Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 7 Nov 2017 15:32:35 +0100
Subject: [PATCH] gnu: Add r-ensembldb.

* gnu/packages/bioinformatics.scm (r-ensembldb): New variable.
---
 gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 227bc34296..b6a3aa9722 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9599,6 +9599,50 @@ filters for manipulating Bioconductor annotation resources.  The filters are
 used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
     (license license:artistic2.0)))
 
+(define-public r-ensembldb
+  (package
+    (name "r-ensembldb")
+    (version "2.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ensembldb" version))
+       (sha256
+        (base32
+         "1w0lca3ws5j770bmls91cn93lznvv2pc8s42nybdzz3vdxjvb4m1"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationfilter" ,r-annotationfilter)
+       ("r-annotationhub" ,r-annotationhub)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-curl" ,r-curl)
+       ("r-dbi" ,r-dbi)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://github.com/jotsetung/ensembldb")
+    (synopsis "Utilities to create and use Ensembl-based annotation databases")
+    (description
+     "The package provides functions to create and use transcript-centric
+annotation databases/packages.  The annotation for the databases are directly
+fetched from Ensembl using their Perl API.  The functionality and data is
+similar to that of the TxDb packages from the @code{GenomicFeatures} package,
+but, in addition to retrieve all gene/transcript models and annotations from
+the database, the @code{ensembldb} package also provides a filter framework
+allowing to retrieve annotations for specific entries like genes encoded on a
+chromosome region or transcript models of lincRNA genes.")
+    ;; No version specified
+    (license license:lgpl3+)))
+
 (define-public r-qvalue
   (package
     (name "r-qvalue")