* [PATCH 1/2] gnu: Add r-rhtslib.
@ 2016-08-18 11:09 Ricardo Wurmus
2016-08-18 11:09 ` [PATCH 2/2] gnu: Add r-bamsignals Ricardo Wurmus
2016-08-21 20:26 ` [PATCH 1/2] gnu: Add r-rhtslib Leo Famulari
0 siblings, 2 replies; 6+ messages in thread
From: Ricardo Wurmus @ 2016-08-18 11:09 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-rhtslib): New variable.
---
gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 233b7a8..ade6e37 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6325,6 +6325,31 @@ two-dimensional genome scans.")
libraries for systems that do not have these available via other means.")
(license license:artistic2.0)))
+(define-public r-rhtslib
+ (package
+ (name "r-rhtslib")
+ (version "1.4.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rhtslib" version))
+ (sha256
+ (base32
+ "1wgpn9x8abjj7fc087pdavqc3fz0pl5xdh231mgjila18irwlhb3"))))
+ (properties `((upstream-name . "Rhtslib")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-zlibbioc" ,r-zlibbioc)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (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 emboss
(package
(name "emboss")
--
2.9.0
^ permalink raw reply related [flat|nested] 6+ messages in thread* [PATCH 2/2] gnu: Add r-bamsignals.
2016-08-18 11:09 [PATCH 1/2] gnu: Add r-rhtslib Ricardo Wurmus
@ 2016-08-18 11:09 ` Ricardo Wurmus
2016-08-21 20:27 ` Leo Famulari
2016-08-21 20:26 ` [PATCH 1/2] gnu: Add r-rhtslib Leo Famulari
1 sibling, 1 reply; 6+ messages in thread
From: Ricardo Wurmus @ 2016-08-18 11:09 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-bamsignals): New variable.
---
gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ade6e37..2bd71c8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6350,6 +6350,36 @@ 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")
+ (version "1.4.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bamsignals" version))
+ (sha256
+ (base32
+ "1xqiqvg52p6fcvhr4146djbz79r3j1kmh75mq7rndwglmiybpwmy"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "http://bioconductor.org/packages/bamsignals")
+ (synopsis "Extract read count signals from bam files")
+ (description
+ "This package allows to efficiently obtain count vectors from indexed bam
+files. It counts the number of nucleotide sequence reads in given genomic
+ranges and it computes reads profiles and coverage profiles. It also handles
+paired-end data.")
+ (license license:gpl2+)))
+
(define-public emboss
(package
(name "emboss")
--
2.9.0
^ permalink raw reply related [flat|nested] 6+ messages in thread* Re: [PATCH 1/2] gnu: Add r-rhtslib.
2016-08-18 11:09 [PATCH 1/2] gnu: Add r-rhtslib Ricardo Wurmus
2016-08-18 11:09 ` [PATCH 2/2] gnu: Add r-bamsignals Ricardo Wurmus
@ 2016-08-21 20:26 ` Leo Famulari
2016-08-22 14:53 ` Ricardo Wurmus
1 sibling, 1 reply; 6+ messages in thread
From: Leo Famulari @ 2016-08-21 20:26 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
On Thu, Aug 18, 2016 at 01:09:41PM +0200, Ricardo Wurmus wrote:
> * gnu/packages/bioinformatics.scm (r-rhtslib): New variable.
LGTM
^ permalink raw reply [flat|nested] 6+ messages in thread
end of thread, other threads:[~2016-08-22 14:54 UTC | newest]
Thread overview: 6+ messages (download: mbox.gz follow: Atom feed
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2016-08-18 11:09 [PATCH 1/2] gnu: Add r-rhtslib Ricardo Wurmus
2016-08-18 11:09 ` [PATCH 2/2] gnu: Add r-bamsignals Ricardo Wurmus
2016-08-21 20:27 ` Leo Famulari
2016-08-22 14:53 ` Ricardo Wurmus
2016-08-21 20:26 ` [PATCH 1/2] gnu: Add r-rhtslib Leo Famulari
2016-08-22 14:53 ` Ricardo Wurmus
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