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[bug#45399,07/10] gnu: r-homo-sapiens: Move to (gnu packages bioconductor).

Message ID 20201223180635.58647-8-zimon.toutoune@gmail.com
State Accepted
Headers show
Series Move some Bioconductor packages to (gnu packages bioconductor). | expand

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Commit Message

Simon Tournier Dec. 23, 2020, 6:06 p.m. UTC 
* 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(-)
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Patch

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"))