From: zimoun <zimon.toutoune@gmail.com>
To: 47171@debbugs.gnu.org
Cc: zimoun <zimon.toutoune@gmail.com>
Subject: [bug#47171] [PATCH 09/10] gnu: r-rsamtools: Move to (gnu packages bioconductor).
Date: Mon, 15 Mar 2021 19:09:03 +0100 [thread overview]
Message-ID: <20210315180904.8346-9-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20210315180904.8346-1-zimon.toutoune@gmail.com>
* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here...
* gnu/packages/bioconductor.scm (r-rsamtools): ...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 2b7d65023d..c659bdd09e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2147,6 +2147,49 @@ reports together for a particular project that can be viewed in a web
browser.")
(license license:artistic2.0)))
+(define-public r-rsamtools
+ (package
+ (name "r-rsamtools")
+ (version "2.6.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rsamtools" version))
+ (sha256
+ (base32
+ "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
+ (properties
+ `((upstream-name . "Rsamtools")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'use-system-zlib
+ (lambda _
+ (substitute* "DESCRIPTION"
+ (("zlibbioc, ") ""))
+ (substitute* "NAMESPACE"
+ (("import\\(zlibbioc\\)") ""))
+ #t)))))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bitops" ,r-bitops)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
+ (synopsis "Interface to samtools, bcftools, and tabix")
+ (description
+ "This package provides an interface to the @code{samtools},
+@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
+Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
+tab-delimited (tabix) files.")
+ (license license:expat)))
+
(define-public r-shortread
(package
(name "r-shortread")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 415210085e..05805d1a8b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,49 +7691,6 @@ including VCF header and contents in RDF and JSON.")
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
-(define-public r-rsamtools
- (package
- (name "r-rsamtools")
- (version "2.6.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "Rsamtools" version))
- (sha256
- (base32
- "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
- (properties
- `((upstream-name . "Rsamtools")))
- (build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'use-system-zlib
- (lambda _
- (substitute* "DESCRIPTION"
- (("zlibbioc, ") ""))
- (substitute* "NAMESPACE"
- (("import\\(zlibbioc\\)") ""))
- #t)))))
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-bitops" ,r-bitops)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rhtslib" ,r-rhtslib)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
- (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
- (synopsis "Interface to samtools, bcftools, and tabix")
- (description
- "This package provides an interface to the @code{samtools},
-@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
-Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
-tab-delimited (tabix) files.")
- (license license:expat)))
-
(define-public r-delayedarray
(package
(name "r-delayedarray")
--
2.30.1
next prev parent reply other threads:[~2021-03-15 18:49 UTC|newest]
Thread overview: 24+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-03-15 18:07 [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor) zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 01/10] gnu: r-limma: Move " zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 02/10] gnu: r-xvector: " zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 03/10] gnu: r-genomicranges: " zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 04/10] gnu: r-biobase: " zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 05/10] gnu: r-annotationdbi: " zimoun
2021-03-15 18:09 ` [bug#47171] [PATCH 06/10] gnu: r-biomart: " zimoun
2021-03-15 18:09 ` [bug#47171] [PATCH 07/10] gnu: r-biocparallel: " zimoun
2021-03-15 18:09 ` [bug#47171] [PATCH 08/10] gnu: r-biostrings: " zimoun
2021-03-15 18:09 ` zimoun [this message]
2021-03-15 18:09 ` [bug#47171] [PATCH 10/10] gnu: r-delayedarray: " zimoun
2021-03-15 22:33 ` bug#47171: [PATCH 00/10] Move some Bioconductor packages " Ricardo Wurmus
2021-03-15 23:56 ` [bug#47171] " Leo Famulari
2021-03-16 12:27 ` zimoun
2021-03-16 13:20 ` Ricardo Wurmus
2021-03-16 13:30 ` zimoun
2021-03-16 16:08 ` Ricardo Wurmus
2021-03-16 16:36 ` zimoun
2021-03-16 22:04 ` Ricardo Wurmus
2021-03-17 20:15 ` zimoun
2021-03-17 20:14 ` [bug#47171] [PATCH v2 1/3] gnu: r-bisquerna: Move " zimoun
2021-03-17 20:14 ` [bug#47171] [PATCH v2 2/3] gnu: r-absfiltergsea: " zimoun
2021-03-17 20:14 ` [bug#47171] [PATCH v2 3/3] Revert "Revert some commits that caused `guix pull` to fail." zimoun
2021-03-31 19:29 ` bug#47171: [PATCH v2 1/3] gnu: r-bisquerna: Move to (gnu packages bioconductor) Ricardo Wurmus
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