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09/10: gnu: r-shortread: Move to (gnu packages bioconductor).
From: |
guix-commits |
Subject: |
09/10: gnu: r-shortread: Move to (gnu packages bioconductor). |
Date: |
Fri, 12 Mar 2021 08:53:11 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 8957efa8ef940685811b9e55eb7178ecd33abb40
Author: zimoun <zimon.toutoune@gmail.com>
AuthorDate: Mon Mar 8 18:58:02 2021 +0100
gnu: r-shortread: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-shortread): Move from here...
* gnu/packages/bioconductor.scm (r-shortread): ...to here.
---
gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 43 -----------------------------------------
2 files changed, 43 insertions(+), 43 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a4618ec..283ae7a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1845,6 +1845,49 @@ reports together for a particular project that can be
viewed in a web
browser.")
(license license:artistic2.0)))
+(define-public r-shortread
+ (package
+ (name "r-shortread")
+ (version "1.48.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ShortRead" version))
+ (sha256
+ (base32
+ "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
+ (properties `((upstream-name . "ShortRead")))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-hwriter" ,r-hwriter)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-latticeextra" ,r-latticeextra)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (home-page "https://bioconductor.org/packages/ShortRead")
+ (synopsis "FASTQ input and manipulation tools")
+ (description
+ "This package implements sampling, iteration, and input of FASTQ files.
+It includes functions for filtering and trimming reads, and for generating a
+quality assessment report. Data are represented as
+@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
+purposes. The package also contains legacy support for early single-end,
+ungapped alignment formats.")
+ (license license:artistic2.0)))
+
(define-public r-geneplotter
(package
(name "r-geneplotter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c4713fc..f363d64 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7387,49 +7387,6 @@ includes software to
")
(license license:cc0))))
-(define-public r-shortread
- (package
- (name "r-shortread")
- (version "1.48.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "ShortRead" version))
- (sha256
- (base32
- "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
- (properties `((upstream-name . "ShortRead")))
- (build-system r-build-system)
- (inputs
- `(("zlib" ,zlib)))
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-rhtslib" ,r-rhtslib)
- ("r-hwriter" ,r-hwriter)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-latticeextra" ,r-latticeextra)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)
- ("r-zlibbioc" ,r-zlibbioc)))
- (home-page "https://bioconductor.org/packages/ShortRead")
- (synopsis "FASTQ input and manipulation tools")
- (description
- "This package implements sampling, iteration, and input of FASTQ files.
-It includes functions for filtering and trimming reads, and for generating a
-quality assessment report. Data are represented as
-@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
-purposes. The package also contains legacy support for early single-end,
-ungapped alignment formats.")
- (license license:artistic2.0)))
-
(define-public r-systempiper
(package
(name "r-systempiper")
- branch master updated (323aec6 -> df6b3c2), guix-commits, 2021/03/12
- 01/10: gnu: r-genefilter: Move to (gnu packages bioconductor)., guix-commits, 2021/03/12
- 02/10: gnu: r-deseq2: Move to (gnu packages bioconductor)., guix-commits, 2021/03/12
- 03/10: gnu: r-dexseq: Move to (gnu packages bioconductor)., guix-commits, 2021/03/12
- 04/10: gnu: r-annotationforge: Move to (gnu packages bioconductor)., guix-commits, 2021/03/12
- 05/10: gnu: r-rbgl: Move to (gnu packages bioconductor)., guix-commits, 2021/03/12
- 07/10: gnu: r-category: Move to (gnu packages bioconductor)., guix-commits, 2021/03/12
- 06/10: gnu: r-gseabase: Move to (gnu packages bioconductor)., guix-commits, 2021/03/12
- 08/10: gnu: r-gostats: Move to (gnu packages bioconductor)., guix-commits, 2021/03/12
- 09/10: gnu: r-shortread: Move to (gnu packages bioconductor).,
guix-commits <=
- 10/10: gnu: r-systempiper: Move to (gnu packages bioconductor)., guix-commits, 2021/03/12