GNU bug report logs -
#48575
[PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor).
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Reported by: zimoun <zimon.toutoune <at> gmail.com>
Date: Fri, 21 May 2021 20:23:01 UTC
Severity: normal
Tags: patch
Done: Ricardo Wurmus <rekado <at> elephly.net>
Bug is archived. No further changes may be made.
Full log
Message #11 received at 48575 <at> debbugs.gnu.org (full text, mbox):
* 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 <rekado <at> elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado <at> elephly.net>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel <at> gnu.org>
;;; Copyright © 2016 Pjotr Prins <pjotr.guix <at> thebird.nl>
;;; Copyright © 2016 Ben Woodcroft <donttrustben <at> gmail.com>
@@ -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
This bug report was last modified 4 years and 47 days ago.
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