[bug#60938] [patch] gnu: Add r-breakpointrdata and r-breakpointr

[bug#60938] [patch] gnu: Add r-breakpointrdata and r-breakpointr

[MadalinIonel.Patrascu]

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[bug#60938] [PATCH 1/2] gnu: Add r-breakpointrdata.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-breakpointrdata): New variable.
---
 gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ca236bcf75..27f8111982 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1291,6 +1291,26 @@ (define-public r-biscuiteerdata
 biscuiteer.")
     (license license:gpl3)))
 
+(define-public r-breakpointrdata
+  (package
+    (name "r-breakpointrdata")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "breakpointRdata" version 'experiment))
+              (sha256
+               (base32
+                "0f23i4ynb4vgn22c3d2l64z92rzv3qnwd4j8qyvalklrxkwilhfn"))))
+    (properties `((upstream-name . "breakpointRdata")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/daewoooo/breakpointRdata")
+    (synopsis "Strand-seq data for demonstration purposes")
+    (description
+     "This packpage is a collection of Strand-seq data.  The main pupose is to
+demonstrate functionalities of breakpointR package.")
+    (license license:expat)))
+
 (define-public r-celldex
   (package
     (name "r-celldex")

base-commit: f088763356e88c4911ee933fdafcad6ed66a7aa3
-- 
2.39.1

[bug#60938] [PATCH 2/2] gnu: Add r-breakpointr.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-breakpointr): New variable.
---
 gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 27f8111982..5a69aecf18 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3500,6 +3500,40 @@ (define-public r-biocgenerics
 packages.")
     (license license:artistic2.0)))
 
+(define-public r-breakpointr
+  (package
+    (name "r-breakpointr")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "breakpointR" version))
+              (sha256
+               (base32
+                "0j1f43lhgkapjyxlil9fflqh9nf3andhmvirdcv45y60wvljn4gx"))))
+    (properties `((upstream-name . "breakpointR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-breakpointrdata
+           r-cowplot
+           r-doparallel
+           r-foreach
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-ggplot2
+           r-gtools
+           r-iranges
+           r-rsamtools
+           r-s4vectors))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/daewoooo/BreakPointR")
+    (synopsis "Find breakpoints in Strand-seq data")
+    (description
+     "This package implements functions for finding breakpoints, plotting and
+export of Strand-seq data.")
+    (license license:expat)))
+
 (define-public r-cardelino
   (package
     (name "r-cardelino")
-- 
2.39.1

bug#60938: [PATCH 2/2] gnu: Add r-breakpointr.

[Ricardo Wurmus]

Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:

> * gnu/packages/bioconductor.scm (r-breakpointrdata): New variable.
> * gnu/packages/bioconductor.scm (r-breakpointr): New variable.

I applied them both after fixing two typos in the description of
r-breakpointrdata.

Thanks!

-- 
Ricardo