Subject: [PATCH 01/50] gnu: r-genomicalignments: Move to (gnu packages bioconductor).

From: zimoun <[email-masked]>
Date: Fri, 21 May 2021 22:25:33 +0200

* gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here...
* gnu/packages/bioconductor.scm (r-genomicalignments): ...to here.
---
 gnu/packages/bioconductor.scm   | 35 ++++++++++++++++++++++++++++++++-
 gnu/packages/bioinformatics.scm | 33 -------------------------------
 2 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 45e31a5760..4f4ff82ad0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <[email-masked]>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <[email-masked]>
 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <[email-masked]>
 ;;; Copyright © 2016 Pjotr Prins <[email-masked]>
 ;;; Copyright © 2016 Ben Woodcroft <[email-masked]>
@@ -2075,6 +2075,39 @@ translation between different chromosome sequence naming conventions (e.g.,
 names in their natural, rather than lexicographic, order.")
     (license license:artistic2.0)))
 
+(define-public r-genomicalignments
+  (package
+    (name "r-genomicalignments")
+    (version "1.26.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GenomicAlignments" version))
+              (sha256
+               (base32
+                "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
+    (properties
+     `((upstream-name . "GenomicAlignments")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://bioconductor.org/packages/GenomicAlignments")
+    (synopsis "Representation and manipulation of short genomic alignments")
+    (description
+     "This package provides efficient containers for storing and manipulating
+short genomic alignments (typically obtained by aligning short reads to a
+reference genome).  This includes read counting, computing the coverage,
+junction detection, and working with the nucleotide content of the
+alignments.")
+    (license license:artistic2.0)))
+
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9c77d66a35..0d0fe1df30 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,39 +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-genomicalignments
-  (package
-    (name "r-genomicalignments")
-    (version "1.26.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "GenomicAlignments" version))
-              (sha256
-               (base32
-                "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
-    (properties
-     `((upstream-name . "GenomicAlignments")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (home-page "https://bioconductor.org/packages/GenomicAlignments")
-    (synopsis "Representation and manipulation of short genomic alignments")
-    (description
-     "This package provides efficient containers for storing and manipulating
-short genomic alignments (typically obtained by aligning short reads to a
-reference genome).  This includes read counting, computing the coverage,
-junction detection, and working with the nucleotide content of the
-alignments.")
-    (license license:artistic2.0)))
-
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-- 
2.30.1