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

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Message #20 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 05/50] gnu: r-bsgenome: Move to (gnu packages bioconductor).
Date: Fri, 21 May 2021 22:25:37 +0200

* gnu/packages/bioinformatics.scm (r-bsgenome): Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome): ...to here.
---
 gnu/packages/bioconductor.scm   | 33 ++++++++++++++++++++++++++++++++-
 gnu/packages/bioinformatics.scm | 31 -------------------------------
 2 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2afb5214ee..923413135b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4,7 +4,7 @@
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix <at> thebird.nl>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben <at> gmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim <at> flashner.co.il>
-;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me <at> tobias.gr>
+;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me <at> tobias.gr>
 ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune <at> gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau <at> gmail.com>
 ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
@@ -1875,6 +1875,37 @@ matching algorithms, and other utilities, for fast manipulation of large
 biological sequences or sets of sequences.")
     (license license:artistic2.0)))
 
+(define-public r-bsgenome
+  (package
+    (name "r-bsgenome")
+    (version "1.58.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BSgenome" version))
+              (sha256
+               (base32
+                "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq"))))
+    (properties
+     `((upstream-name . "BSgenome")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (home-page "https://bioconductor.org/packages/BSgenome")
+    (synopsis "Infrastructure for Biostrings-based genome data packages")
+    (description
+     "This package provides infrastructure shared by all Biostrings-based
+genome data packages and support for efficient SNP representation.")
+    (license license:artistic2.0)))
+
 (define-public r-category
   (package
     (name "r-category")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 32d2b6a683..9c9288c6b0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7873,37 +7873,6 @@ including VCF header and contents in RDF and JSON.")
 information about the latest version of the Gene Ontologies.")
     (license license:artistic2.0)))
 
-(define-public r-bsgenome
-  (package
-    (name "r-bsgenome")
-    (version "1.58.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "BSgenome" version))
-              (sha256
-               (base32
-                "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq"))))
-    (properties
-     `((upstream-name . "BSgenome")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (home-page "https://bioconductor.org/packages/BSgenome")
-    (synopsis "Infrastructure for Biostrings-based genome data packages")
-    (description
-     "This package provides infrastructure shared by all Biostrings-based
-genome data packages and support for efficient SNP representation.")
-    (license license:artistic2.0)))
-
 (define-public r-impute
   (package
     (name "r-impute")
-- 
2.30.1

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