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

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Package: guix-patches;

Reported by: "MadalinIonel.Patrascu <at> mdc-berlin.de" <MadalinIonel.Patrascu <at> mdc-berlin.de>

Date: Wed, 18 Jan 2023 17:34:02 UTC

Severity: normal

Tags: patch

Done: Ricardo Wurmus <rekado <at> elephly.net>

Bug is archived. No further changes may be made.

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Report forwarded to guix-patches <at> gnu.org:
bug#60938; Package guix-patches. (Wed, 18 Jan 2023 17:34:02 GMT) Full text and rfc822 format available.

Acknowledgement sent to "MadalinIonel.Patrascu <at> mdc-berlin.de" <MadalinIonel.Patrascu <at> mdc-berlin.de>:
New bug report received and forwarded. Copy sent to guix-patches <at> gnu.org. (Wed, 18 Jan 2023 17:34:02 GMT) Full text and rfc822 format available.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: "MadalinIonel.Patrascu <at> mdc-berlin.de"
 <MadalinIonel.Patrascu <at> mdc-berlin.de>
To: "guix-patches <at> gnu.org" <guix-patches <at> gnu.org>
Subject: [patch] gnu: Add r-breakpointrdata and r-breakpointr
Date: Wed, 18 Jan 2023 17:33:14 +0000
[Message part 1 (text/plain, inline)]

[Message part 2 (text/html, inline)]

Information forwarded to rekado <at> elephly.net, guix-patches <at> gnu.org:
bug#60938; Package guix-patches. (Wed, 18 Jan 2023 17:37:02 GMT) Full text and rfc822 format available.

Message #8 received at 60938 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <60938 <at> debbugs.gnu.org>
Subject: [PATCH 1/2] gnu: Add r-breakpointrdata.
Date: Wed, 18 Jan 2023 18:35:58 +0100
* 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





Information forwarded to rekado <at> elephly.net, guix-patches <at> gnu.org:
bug#60938; Package guix-patches. (Wed, 18 Jan 2023 17:37:02 GMT) Full text and rfc822 format available.

Message #11 received at 60938 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <60938 <at> debbugs.gnu.org>
Subject: [PATCH 2/2] gnu: Add r-breakpointr.
Date: Wed, 18 Jan 2023 18:35:59 +0100
* 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





Reply sent to Ricardo Wurmus <rekado <at> elephly.net>:
You have taken responsibility. (Wed, 18 Jan 2023 21:48:02 GMT) Full text and rfc822 format available.

Notification sent to "MadalinIonel.Patrascu <at> mdc-berlin.de" <MadalinIonel.Patrascu <at> mdc-berlin.de>:
bug acknowledged by developer. (Wed, 18 Jan 2023 21:48:02 GMT) Full text and rfc822 format available.

Message #16 received at 60938-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 60938-done <at> debbugs.gnu.org
Subject: Re: [bug#60938] [PATCH 2/2] gnu: Add r-breakpointr.
Date: Wed, 18 Jan 2023 22:46:30 +0100
Mădălin Ionel Patrașcu <madalinionel.patrascu <at> 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




bug archived. Request was from Debbugs Internal Request <help-debbugs <at> gnu.org> to internal_control <at> debbugs.gnu.org. (Thu, 16 Feb 2023 12:24:08 GMT) Full text and rfc822 format available.

This bug report was last modified 1 year and 42 days ago.

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