[PATCH 1/2] gnu: Add r-rhtslib.

[PATCH 1/2] gnu: Add r-rhtslib.

[Ricardo Wurmus]

* 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

[PATCH 2/2] gnu: Add r-bamsignals.

[Ricardo Wurmus]

* 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

Re: [PATCH 1/2] gnu: Add r-rhtslib.

[Leo Famulari]

On Thu, Aug 18, 2016 at 01:09:41PM +0200, Ricardo Wurmus wrote:
> * gnu/packages/bioinformatics.scm (r-rhtslib): New variable.

LGTM

Re: [PATCH 2/2] gnu: Add r-bamsignals.

[Leo Famulari]

On Thu, Aug 18, 2016 at 01:09:42PM +0200, Ricardo Wurmus wrote:
> * gnu/packages/bioinformatics.scm (r-bamsignals): New variable.

LGTM

Re: [PATCH 2/2] gnu: Add r-bamsignals.

[Ricardo Wurmus]

Leo Famulari <leo@famulari.name> writes:

> On Thu, Aug 18, 2016 at 01:09:42PM +0200, Ricardo Wurmus wrote:
>> * gnu/packages/bioinformatics.scm (r-bamsignals): New variable.
>
> LGTM

Thanks.  Pushed as fe02c4c98aee859f7eb75e7ca18a78498ba7fa78.

~~ Ricardo

Re: [PATCH 1/2] gnu: Add r-rhtslib.

[Ricardo Wurmus]

Leo Famulari <leo@famulari.name> writes:

> On Thu, Aug 18, 2016 at 01:09:41PM +0200, Ricardo Wurmus wrote:
>> * gnu/packages/bioinformatics.scm (r-rhtslib): New variable.
>
> LGTM

Thanks.  Pushed as 52765a63ca43a66137272e9826553c072c1ef769.

~~ Ricardo