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From: zimoun <zimon.toutoune@gmail.com>
To: 45399@debbugs.gnu.org
Subject: [bug#45399] [PATCH 07/10] gnu: r-homo-sapiens: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:32 +0100	[thread overview]
Message-ID: <20201223180635.58647-8-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com>

* gnu/packages/bioinformatics.scm (r-homo-sapiens): Move from here...
* gnu/packages/bioconductor.scm (r-homo-sapiens): ...to here.
Replace 'string-append' by 'bioconductor-uri' with 'annotation'.
---
 gnu/packages/bioconductor.scm   | 27 +++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 32 --------------------------------
 2 files changed, 27 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 466bb71101..3b8dce30e5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -389,6 +389,33 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
 in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-homo-sapiens
+  (package
+    (name "r-homo-sapiens")
+    (version "1.3.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
+              (sha256
+               (base32
+                "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
+    (properties
+     `((upstream-name . "Homo.sapiens")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-go-db" ,r-go-db)
+       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
+       ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
+       ("r-organismdbi" ,r-organismdbi)
+       ("r-annotationdbi" ,r-annotationdbi)))
+    (home-page "https://bioconductor.org/packages/Homo.sapiens/")
+    (synopsis "Annotation package for the Homo.sapiens object")
+    (description
+     "This package contains the Homo.sapiens object to access data from
+several related annotation packages.")
+    (license license:artistic2.0)))
+
 (define-public r-org-ce-eg-db
   (package
     (name "r-org-ce-eg-db")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1c59d7a690..2a6ac38505 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10623,38 +10623,6 @@ and more.")
 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
     (license license:gpl3)))
 
-(define-public r-homo-sapiens
-  (package
-    (name "r-homo-sapiens")
-    (version "1.3.1")
-    (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://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "Homo.sapiens_"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
-    (properties
-     `((upstream-name . "Homo.sapiens")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-go-db" ,r-go-db)
-       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
-       ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
-       ("r-organismdbi" ,r-organismdbi)
-       ("r-annotationdbi" ,r-annotationdbi)))
-    (home-page "https://bioconductor.org/packages/Homo.sapiens/")
-    (synopsis "Annotation package for the Homo.sapiens object")
-    (description
-     "This package contains the Homo.sapiens object to access data from
-several related annotation packages.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.29.2





  parent reply	other threads:[~2020-12-23 18:07 UTC|newest]

Thread overview: 14+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2020-12-23 18:03 [bug#45399] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor) zimoun
2020-12-23 18:06 ` zimoun
2020-12-23 18:06   ` [bug#45399] [PATCH 01/10] gnu: r-sushi: Move " zimoun
2020-12-23 18:06   ` [bug#45399] [PATCH 02/10] gnu: r-gwascat: " zimoun
2020-12-23 18:06   ` [bug#45399] [PATCH 03/10] gnu: r-gviz: " zimoun
2020-12-23 18:06   ` [bug#45399] [PATCH 04/10] gnu: r-gqtlstats: " zimoun
2020-12-23 18:06   ` [bug#45399] [PATCH 05/10] gnu: r-ldblock: " zimoun
2020-12-23 18:06   ` [bug#45399] [PATCH 06/10] gnu: r-erma: " zimoun
2020-12-23 18:06   ` zimoun [this message]
2020-12-23 18:06   ` [bug#45399] [PATCH 08/10] gnu: r-snpstats: " zimoun
2020-12-23 18:06   ` [bug#45399] [PATCH 09/10] gnu: r-gqtlstats: " zimoun
2020-12-23 18:06   ` [bug#45399] [PATCH 10/10] gnu: r-ggbio: " zimoun
2020-12-29 16:42 ` bug#45399: [PATCH 00/10] Move some Bioconductor packages " Ricardo Wurmus
2020-12-30  9:13   ` [bug#45399] " zimoun

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