From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <62297@debbugs.gnu.org>
Cc: rekado@elephly.net
Subject: [bug#62297] [PATCH 5/5] gnu: Add r-annotationhubdata.
Date: Mon, 20 Mar 2023 17:00:05 +0100 [thread overview]
Message-ID: <20230320160005.1594550-5-madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <20230320160005.1594550-1-madalinionel.patrascu@mdc-berlin.de>
* 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
next prev parent reply other threads:[~2023-03-20 16:04 UTC|newest]
Thread overview: 7+ messages / expand[flat|nested] mbox.gz Atom feed top
2023-03-20 15:57 [bug#62297] [PATCH] gnu: Add r-affyilm, r-affyplm, r-affylmgui, r-annotationhubdata and r-tkrplot MadalinIonel.Patrascu
2023-03-20 16:00 ` [bug#62297] [PATCH 1/5] gnu: Add r-affyilm Mădălin Ionel Patrașcu
2023-03-20 16:00 ` [bug#62297] [PATCH 2/5] gnu: Add r-affyplm Mădălin Ionel Patrașcu
2023-03-20 16:00 ` [bug#62297] [PATCH 3/5] gnu: Add r-tkrplot Mădălin Ionel Patrașcu
2023-03-20 16:00 ` [bug#62297] [PATCH 4/5] gnu: Add r-affylmgui Mădălin Ionel Patrașcu
2023-03-20 16:00 ` Mădălin Ionel Patrașcu [this message]
2023-03-20 18:33 ` bug#62297: [PATCH 1/5] gnu: Add r-affyilm Ricardo Wurmus
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