GNU bug report logs - #58827
[PATCH] gnu: Add r-dama and r-damefinder.

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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-dama and r-damefinder.
Date: Fri, 28 Oct 2022 02:49:08 +0000

[Message part 1 (text/plain, inline)]

* gnu/packages/bioconductor.scm ( r-dama and r-damefinder): New variables.


Unrelated patches, added in the alphabetical order.


All the best,

     Mădălin-Ionel!

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

Message #8 received at 58827 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <58827 <at> debbugs.gnu.org>
Subject: [PATCH 2/2] gnu: Add r-damefinder.
Date: Fri, 28 Oct 2022 04:53:53 +0200

* gnu/packages/bioconductor.scm (r-damefinder): New variable.
---
 gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9f79954d8d..81918e4fe6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3036,6 +3036,47 @@ (define-public r-dama
 microarray data.")
     (license license:gpl2+)))
 
+(define-public r-damefinder
+  (package
+    (name "r-damefinder")
+    (version "1.8.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "DAMEfinder" version))
+              (sha256
+               (base32
+                "123ra94bij0m45j2fzqr7fjipj4ld9kgk0kir1zfdbbd5h8h4mdf"))))
+    (properties `((upstream-name . "DAMEfinder")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-biostrings
+           r-bumphunter
+           r-cowplot
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-ggplot2
+           r-iranges
+           r-limma
+           r-plyr
+           r-readr
+           r-reshape2
+           r-rsamtools
+           r-s4vectors
+           r-stringr
+           r-summarizedexperiment
+           r-variantannotation))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/DAMEfinder")
+    (synopsis "Differential allelicly methylated regions")
+    (description
+     "This package offers functionality for taking methtuple or @code{bismark}
+outputs to calculate @acronym{ASM, Allele-Specific Methylation} scores and compute
+@acronym{DAMEs, Differential Allelicly MEthylated regions}.  It also offers nice
+visualization of methyl-circle plots.")
+    (license license:expat)))
+
 (define-public r-dearseq
   (package
     (name "r-dearseq")
-- 
2.38.0

Message #11 received at 58827 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <58827 <at> debbugs.gnu.org>
Subject: [PATCH 1/2] gnu: Add r-dama.
Date: Fri, 28 Oct 2022 04:53:52 +0200

* gnu/packages/bioconductor.scm (r-dama): New variable.
---
 gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b8535250f9..9f79954d8d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3013,6 +3013,29 @@ (define-public r-cummerbund
 used visualizations.")
    (license license:artistic2.0)))
 
+(define-public r-dama
+  (package
+    (name "r-dama")
+    (version "1.68.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "daMA" version))
+              (sha256
+               (base32
+                "1mpjvl24wsdmpgra3iasgfvy29m71318gj6j1gg6081w0n4cq72m"))))
+    (properties `((upstream-name . "daMA")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-mass))
+    (home-page "https://bioconductor.org/packages/release/bioc/html/daMA.html")
+             ;; http://www.microarrays.med.uni-goettingen.de - domain not found
+    (synopsis
+     "Efficient design and analysis of factorial two-colour microarray data")
+    (description
+     "This package contains functions for the efficient design of factorial two-
+colour microarray experiments and for the statistical analysis of factorial
+microarray data.")
+    (license license:gpl2+)))
+
 (define-public r-dearseq
   (package
     (name "r-dearseq")

base-commit: ac51b9c86d58cfdb13ee643a2fdc8e979939a260
-- 
2.38.0

Message #16 received at 58827-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: 58827-done <at> debbugs.gnu.org
Subject: Re: [bug#58827] [PATCH 1/2] gnu: Add r-dama.
Date: Fri, 28 Oct 2022 15:13:56 +0200

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

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

Applied, thanks!

-- 
Ricardo

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