GNU bug report logs - #48575
[PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor).

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Message #44 received at 48575 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 48575 <at> debbugs.gnu.org.
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 13/50] gnu: r-genomationdata: Move to (gnu packages
 bioconductor).
Date: Fri, 21 May 2021 22:25:45 +0200

* gnu/packages/bioinformatics.scm (r-genomationdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomationdata): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'experiment.
---
 gnu/packages/bioconductor.scm   | 26 ++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 28 ----------------------------
 2 files changed, 26 insertions(+), 28 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2be7920770..22b5a6068e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1021,6 +1021,32 @@ chromstaR package.")
 genomes and gene ID formats, largely based on the UCSC table browser.")
     (license license:lgpl2.0+)))
 
+(define-public r-genomationdata
+  (package
+    (name "r-genomationdata")
+    (version "1.22.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "genomationData" version 'experiment))
+              (sha256
+               (base32
+                "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
+    (properties
+     `((upstream-name . "genomationData")))
+    (build-system r-build-system)
+    ;; As this package provides little more than large data files, it doesn't
+    ;; make sense to build substitutes.
+    (arguments `(#:substitutable? #f))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
+    (synopsis "Experimental data for use with the genomation package")
+    (description
+     "This package contains experimental genetic data for use with the
+genomation package.  Included are Chip Seq, Methylation and Cage data,
+downloaded from Encode.")
+    (license license:gpl3+)))
+
 (define-public r-pasilla
   (package
     (name "r-pasilla")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f8e7b2cab9..87254a9058 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,34 +7849,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-genomationdata
-  (package
-    (name "r-genomationdata")
-    (version "1.22.0")
-    (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/experiment/src/contrib/"
-                                  "genomationData_" version ".tar.gz"))
-              (sha256
-               (base32
-                "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
-    (build-system r-build-system)
-    ;; As this package provides little more than large data files, it doesn't
-    ;; make sense to build substitutes.
-    (arguments `(#:substitutable? #f))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
-    (synopsis "Experimental data for use with the genomation package")
-    (description
-     "This package contains experimental genetic data for use with the
-genomation package.  Included are Chip Seq, Methylation and Cage data,
-downloaded from Encode.")
-    (license license:gpl3+)))
-
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")
-- 
2.30.1

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