GNU bug report logs - #60958
[PATCH 2/2] gnu: Add r-scds.

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

From: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH 2/2] gnu: Add r-scds.
Date: Fri, 20 Jan 2023 09:58:00 +0100

* gnu/packages/bioconductor.scm (r-scds): New variable.
---
 gnu/packages/bioconductor.scm   | 28 ++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm |  2 +-
 2 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 93c6165b62..bdbdeecc35 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12,6 +12,7 @@
 ;;; Copyright © 2021 Hong Li <hli <at> mdc-berlin.de>
 ;;; Copyright © 2021 Tim Howes <timhowes <at> lavabit.com>
 ;;; Copyright © 2021 Nicolas Vallet <nls.vallet <at> gmail.com>
+;;; Copyright © 2023 Navid Afkhami <Navid.Afkhami <at> mdc-berlin.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -7678,6 +7679,33 @@ (define-public r-trajectoryutils
 structures to hold pseudotime inference results.")
     (license license:gpl3)))
 
+(define-public r-scds
+  (package
+    (name "r-scds")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "scds" version))
+              (sha256
+               (base32
+                "0zdf9yf5s0l8ma7d8yhi7bjd964yj84f5h6aq2p0sypjlnc515hd"))))
+    (properties `((upstream-name . "scds")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-dplyr
+                             r-matrix
+                             r-proc
+                             r-s4vectors
+                             r-singlecellexperiment
+                             r-summarizedexperiment
+                             r-xgboost))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/scds")
+    (synopsis "In-silico doublet annotation for single cell RNA sequencing data")
+    (description
+     "This is an R package for doublet annotation of single cell RNA sequencing data.  
+@code{scds} provides methods to annotate doublets in scRNA-seq data computationally.")
+    (license license:expat)))
+
 (define-public r-slingshot
   (package
    (name "r-slingshot")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 86d65d2031..70ac252a8c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -23,7 +23,7 @@
 ;;; Copyright © 2021 Hong Li <hli <at> mdc-berlin.de>
 ;;; Copyright © 2021, 2022, 2023 Simon Tournier <zimon.toutoune <at> gmail.com>
 ;;; Copyright © 2021 Felix Gruber <felgru <at> posteo.net>
-;;; Copyright © 2022 Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
+;;; Copyright © 2022,2023 Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
 ;;; Copyright © 2022 Antero Mejr <antero <at> mailbox.org>
 ;;;
 ;;; This file is part of GNU Guix.
-- 
2.34.1

Message #10 received at 60958-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 60958-done <at> debbugs.gnu.org
Subject: [PATCH 2/2] gnu: Add r-scds.
Date: Fri, 20 Jan 2023 11:08:25 +0100

Thanks for the patch!

I trimmed off the changes to bioinformatics.scm and moved the change to
the copyright line to patch #60958 where you modified that file.

Applied!

-- 
Ricardo

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