GNU bug report logs - #67147
[PATCH 1/2] gnu: Add r-illuminahumanmethylationepicmanifest.

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

From: nafkhamdc <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: nafkhamdc <navid.afkhami <at> mdc-berlin.de>
Subject: [PATCH 1/2] gnu: Add r-illuminahumanmethylationepicmanifest.
Date: Mon, 13 Nov 2023 12:34:43 +0000

* gnu/packages/bioinformatics.scm (r-illuminahumanmethylationepicmanifest): New variable.

Change-Id: I9635033ed5e7e44ecfaff76cd002379582900686
---
 gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7feea35d74..b99a343dbc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15657,6 +15657,38 @@ (define-public r-giotto
 spatial single-cell expression data.")
       (license license:expat))))
 
+(define-public r-illuminahumanmethylationepicmanifest
+  (let ((commit "a9ffbad36f5e496ece6c4c37b80e2f4f7e02d0c3")
+        (revision "1"))
+    (package
+      (name "r-illuminahumanmethylationepicmanifest")
+      (version (git-version "1.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url
+                "https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0v8f0hl0v8gwi61vgqw56rn5j09h95hj54rb8pzbn0znm162n4fc"))))
+      (properties `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
+      (build-system r-build-system)
+      (home-page
+       "https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest")
+      (synopsis "Illumina Human Methylation Manifest 1.0 B5 for R and minfi")
+      (description
+       "It's a drop-in replacement for the @code{IlluminaHumanMethylationEPIC} package.
+It utilizes a Manifest based on 1.0B5 annotation.  As of version 0.3.0,
+the @code{IlluminaHumanMethylationEPIC} package by Author: Kasper Daniel
+Hansen [cre, aut] still employs the 1.0B2 annotation manifest.  A corresponding
+annotation package, @code{IlluminaHumanMethylationEPICanno.ilm10b5.hg38},
+is available to ensure proper annotation.  The decision to maintain the same
+name is due to complications in downstream processing caused by array name
+lookup in certain preprocessing options.")
+      (license license:artistic2.0))))
+
 (define-public r-illuminahumanmethylationepicanno-ilm10b5-hg38
   (let ((commit "3db06910e27f626e0cc8b335ff45cf9a4050a36a")
         (revision "1"))

base-commit: 77386bdbfe6b0c649c05ab37f08051d1ab3e5074
-- 
2.34.1

Message #10 received at 67147-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 67147-done <at> debbugs.gnu.org
Subject: [PATCH 1/2] gnu: Add r-illuminahumanmethylationepicmanifest.
Date: Mon, 13 Nov 2023 14:47:49 +0100

Thanks for the patch!  I renamed the variable to
r-illuminahumanmethylationepicmanifest-latest and dropped patch #67148
in favor of this modified patch.

Pushed to master with commit 951a1433f38a7cffa4cbcb4065c27494c300f2fa.

-- 
Ricardo

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