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[bug#48575] [PATCH 39/50] gnu: r-rhtslib: Move to (gnu packages biocondu
From: |
zimoun |
Subject: |
[bug#48575] [PATCH 39/50] gnu: r-rhtslib: Move to (gnu packages bioconductor). |
Date: |
Fri, 21 May 2021 22:26:11 +0200 |
* gnu/packages/bioinformatics.scm (r-rhtslib): Move from here...
* gnu/packages/bioconductor.scm (r-rhtslib): ...to here.
---
gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 31 -------------------------------
2 files changed, 32 insertions(+), 31 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e720d7bf6a..8e78a2a0ca 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -39,6 +39,7 @@
#:use-module (gnu packages boost)
#:use-module (gnu packages cran)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages curl)
#:use-module (gnu packages gcc)
#:use-module (gnu packages graph)
#:use-module (gnu packages graphviz)
@@ -2832,6 +2833,37 @@ Enrichment Analysis} (GSEA).")
the Human Protein Atlas project.")
(license license:artistic2.0)))
+(define-public r-rhtslib
+ (package
+ (name "r-rhtslib")
+ (version "1.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rhtslib" version))
+ (sha256
+ (base32
+ "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4"))))
+ (properties `((upstream-name . "Rhtslib")))
+ (build-system r-build-system)
+ ;; Without this a temporary directory ends up in the Rhtslib.so binary,
+ ;; which makes R abort the build.
+ (arguments '(#:configure-flags '("--no-staged-install")))
+ (propagated-inputs
+ `(("curl" ,curl)
+ ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)
+ ("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/nhayden/Rhtslib")
+ (synopsis "High-throughput sequencing library as an R package")
+ (description
+ "This package provides the HTSlib C library for high-throughput
+nucleotide sequence analysis. The package is primarily useful to developers
+of other R packages who wish to make use of HTSlib.")
+ (license license:lgpl2.0+)))
+
(define-public r-impute
(package
(name "r-impute")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 39c437f4a2..586efcf21e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7872,37 +7872,6 @@ including VCF header and contents in RDF and JSON.")
secondary structure and comparative analysis in R.")
(license license:gpl3+)))
-(define-public r-rhtslib
- (package
- (name "r-rhtslib")
- (version "1.22.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "Rhtslib" version))
- (sha256
- (base32
- "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4"))))
- (properties `((upstream-name . "Rhtslib")))
- (build-system r-build-system)
- ;; Without this a temporary directory ends up in the Rhtslib.so binary,
- ;; which makes R abort the build.
- (arguments '(#:configure-flags '("--no-staged-install")))
- (propagated-inputs
- `(("curl" ,curl)
- ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
- ("r-zlibbioc" ,r-zlibbioc)))
- (native-inputs
- `(("pkg-config" ,pkg-config)
- ("r-knitr" ,r-knitr)))
- (home-page "https://github.com/nhayden/Rhtslib")
- (synopsis "High-throughput sequencing library as an R package")
- (description
- "This package provides the HTSlib C library for high-throughput
-nucleotide sequence analysis. The package is primarily useful to developers
-of other R packages who wish to make use of HTSlib.")
- (license license:lgpl2.0+)))
-
(define-public r-bamsignals
(package
(name "r-bamsignals")
--
2.30.1
- [bug#48575] [PATCH 29/50] gnu: r-affyio: Move to (gnu packages bioconductor)., (continued)
- [bug#48575] [PATCH 29/50] gnu: r-affyio: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 41/50] gnu: r-rcas: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 42/50] gnu: r-mutationalpatterns: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 44/50] gnu: r-rhdf5filters: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 48/50] gnu: r-copyhelper: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 46/50] gnu: r-rhdf5: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 45/50] gnu: r-annotationfilter: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 47/50] gnu: r-chipseq: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 50/50] gnu: r-methylkit: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 49/50] gnu: r-copywriter: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- [bug#48575] [PATCH 39/50] gnu: r-rhtslib: Move to (gnu packages bioconductor).,
zimoun <=
- [bug#48575] [PATCH 40/50] gnu: r-bamsignals: Move to (gnu packages bioconductor)., zimoun, 2021/05/21
- bug#48575: [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor)., Ricardo Wurmus, 2021/05/31