[bug#68833] [PATCH] gnu: Add r-hmmcopy.

[bug#68833] [PATCH] gnu: Add r-hmmcopy.

[Spencer King]

[-- Attachment #1: Type: text/plain, Size: 1076 bytes --]



-- 
CONFIDENTIALITY NOTICE: This email and any attachments are for the 
exclusive and confidential use which may include protected health 
information for the intended recipient. If you are not the intended 
recipient, any use or disclosure of this information is strictly 
prohibited. You are requested to not disseminate, distribute or copy this 
communication. Please notify the sender immediately if you have received 
this communication in error and delete or destroy this e-mail and any 
attachments. Communications cannot be guaranteed to be secured or 
error-free as information could be intercepted, corrupted, lost, destroyed, 
arrive late or incomplete, or contain viruses. The sender does not accept 
liability for any errors or omissions in the contents of this communication 
which arise as a result of transmission. If verification is required please 
request a hard-copy version of the e-mail and any attachments. Geneoscopy, 
2220 Welsch Industrial Ct., St. Louis, MO 63146, http://www.geneoscopy.com 
<http://www.geneoscopy.com> (2023)

[-- Attachment #2: 0001-gnu-Add-r-hmmcopy.patch --]
[-- Type: application/octet-stream, Size: 2236 bytes --]

From aa3cf7e7962332d238249328d9cac5bfc047aaf5 Mon Sep 17 00:00:00 2001
Message-Id: <aa3cf7e7962332d238249328d9cac5bfc047aaf5.1706655404.git.spencer.king@geneoscopy.com>
From: Spencer King <spencer.king@geneoscopy.com>
Date: Tue, 30 Jan 2024 22:44:57 +0000
Subject: [PATCH] gnu: Add r-hmmcopy.

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

Change-Id: Iface547e865609427c356277edc904f3aec386d8
---
 gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index de0005b523..0a9419cc3e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13,6 +13,7 @@
 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
 ;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com>
 ;;; Copyright © 2023 Navid Afkhami <Navid.Afkhami@mdc-berlin.de>
+;;; Copyright © 2024 Spencer King <spencer.king@geneoscopy.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -14113,6 +14114,29 @@ (define-public r-dnacopy
 abnormal copy number.")
     (license license:gpl2+)))
 
+(define-public r-hmmcopy
+  (package
+    (name "r-hmmcopy")
+    (version "1.44.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "HMMcopy" version))
+       (sha256
+        (base32 "1nhm8bv6p5zcs7f9p1hqzyjgya6v3q8rl13blh135pk9gxjiad2c"))))
+    (properties `((upstream-name . "HMMcopy")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-data-table))
+    (home-page "https://bioconductor.org/packages/HMMcopy")
+    (synopsis
+     "Copy number prediction with correction for GC and mappability bias for HTS data")
+    (description
+     "Corrects GC and mappability biases for readcounts (i.e.  coverage) in
+non-overlapping windows of fixed length for single whole genome samples,
+yielding a rough estimate of copy number for furthur analysis.  Designed for
+rapid correction of high coverage whole genome tumour and normal samples.")
+    (license license:gpl3)))
+
 ;; This is a CRAN package, but it uncharacteristically depends on a
 ;; Bioconductor package.
 (define-public r-htscluster

base-commit: bed3a0b547a59f63b545db165e76ddd9af8bba1a
-- 
2.34.1

[bug#68833]

[King, Spencer via Guix-patches via]

Hello, 

This is Spencer again. I just wanted to follow up on this patch from a different email address. The initial patch was sent using my work email and I was unaware that confidentiality notice would be added on outgoing messages. I just wanted to clarify that the patch was intended to be sent to the issue tracker and is not confidential. If you need me to resubmit from an address that doesn't add that notice I am happy to do so. I just wanted to clear up any potential confusion caused by that notice.

Best,
Spencer