Subject: [bug#62297] [PATCH 5/5] gnu: Add r-annotationhubdata.

From: Mădălin Ionel Patrașcu<[email-masked]>
Date: Mon, 20 Mar 2023 17:00:05 +0100

* gnu/packages/bioconductor.scm (r-annotationhubdata): New variable.
---
 gnu/packages/bioconductor.scm | 53 +++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 78ce740c2c..8ebdcc3706 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2704,6 +2704,59 @@ (define-public r-animalcules
 to understand their data better and discover new insights.")
     (license license:artistic2.0)))
 
+(define-public r-annotationhubdata
+  (package
+    (name "r-annotationhubdata")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "AnnotationHubData" version))
+       (sha256
+        (base32 "0mcx09kcxccw2gkf4c3w7sxgb7v3gwbvahvx9wgq8f93q85yzg95"))))
+    (properties `((upstream-name . "AnnotationHubData")))
+    (build-system r-build-system)
+    (arguments
+      (list
+      #:phases
+      #~(modify-phases %standard-phases
+         (add-before 'install 'change-home-dir
+           (lambda _
+             ;; Change from /homeless-shelter to /tmp for write permission.
+             (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list r-annotationdbi
+           r-annotationforge
+           r-annotationhub
+           r-biobase
+           r-bioccheck
+           r-biocgenerics
+           r-biocmanager
+           r-biocviews
+           r-biostrings
+           r-dbi
+           r-futile-logger
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-graph
+           r-iranges
+           r-jsonlite
+           r-organismdbi
+           r-rcurl
+           r-rsamtools
+           r-rsqlite
+           r-rtracklayer
+           r-s4vectors
+           r-xml))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/AnnotationHubData")
+    (synopsis "Transform public data resources into Bioconductor data structures")
+    (description
+     "These recipes convert a wide variety and a growing number of public bioinformatic
+data sets into easily-used standard Bioconductor data structures.")
+    (license license:artistic2.0)))
+
 (define-public r-anvil
   (package
     (name "r-anvil")
-- 
2.39.2