GNU bug report logs - #58806
[PATCH] gnu: Add r-baalchip.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#58806: closed ([PATCH] gnu: Add r-baalchip.)
Date: Thu, 27 Oct 2022 11:56:02 +0000

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Your message dated Thu, 27 Oct 2022 13:55:00 +0200
with message-id <87o7txiiqj.fsf <at> elephly.net>
and subject line [PATCH] gnu: Add r-baalchip.
has caused the debbugs.gnu.org bug report #58806,
regarding [PATCH] gnu: Add r-baalchip.
to be marked as done.

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help-debbugs <at> gnu.org.)


-- 
58806: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=58806
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From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-baalchip.
Date: Thu, 27 Oct 2022 00:38:09 +0200

 X-Debbugs-Cc: rekado <at> elephly.net

* gnu/packages/bioconductor.scm (r-baalchip): New variable.
---
 gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3692bb94af..23991983da 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2293,6 +2293,51 @@ (define-public r-antiprofiles
 tumor samples from healthy controls.")
     (license license:artistic2.0)))
 
+(define-public r-baalchip
+  (package
+    (name "r-baalchip")
+    (version "1.22.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BaalChIP" version))
+              (sha256
+               (base32
+                "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q"))))
+    (properties `((upstream-name . "BaalChIP")))
+    (build-system r-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-HOME
+           (lambda _ (setenv "HOME" "/tmp"))))))
+    (inputs (list perl))  ;; extra/get.overlaps.v2_chrXY.perl
+    (propagated-inputs
+     (list r-coda
+           r-doby
+           r-doparallel
+           r-foreach
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-ggplot2
+           r-iranges
+           r-reshape2
+           r-rsamtools
+           r-scales))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/BaalChIP")
+    (synopsis
+     "Analysis of allele-specific transcription factor binding in cancer genomes")
+    (description
+     "The package offers functions to process multiple @code{ChIP-seq BAM} files
+and detect allele-specific events.  Computes allele counts at individual variants
+(SNPs/SNVs), implements extensive @dfn{QC} (quality control) steps to remove
+problematic variants, and utilizes a Bayesian framework to identify statistically
+significant allele-specific events.  @code{BaalChIP} is able to account for copy
+number differences between the two alleles, a known phenotypical feature of cancer
+samples.")
+    (license license:artistic2.0)))
+
 (define-public r-biocversion
   (package
     (name "r-biocversion")

base-commit: a2e4e3489b4fdec6e270c93fcd9724abe983217e
-- 
2.37.3

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: 58806-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-baalchip.
Date: Thu, 27 Oct 2022 13:55:00 +0200

Applied with minor changes.  Thanks!

-- 
Ricardo

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