GNU bug report logs - #71651
[PATCH] gnu: Add r-anpan.

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

From: "Afkhami, Navid" <Navid.Afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: "Afkhami, Navid" <Navid.Afkhami <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add r-anpan.
Date: Wed, 19 Jun 2024 15:02:46 +0000

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

Change-Id: Ia01ba3be7424306674b9c9b2904f1f0cfa66d818
---
 gnu/packages/bioinformatics.scm | 48 +++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e2632a5aa4..8ffc46d86d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -752,6 +752,54 @@ (define-public r-anndatar
 @code{SingleCellExperiment} and Seurat objects.")
       (license license:expat))))
 
+(define-public r-anpan
+  (let ((commit "286b88dcf5e9e963a595482139aade154ee1dc86")
+        (revision "1"))
+    (package
+      (name "r-anpan")
+      (version (git-version "0.3.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/biobakery/anpan")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "10nw5v69gn4pxb4g5gd8nh9r1ywd6yczapl3dpdfms0434wcmkxm"))))
+      (properties `((upstream-name . "anpan")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-ape
+                               r-cmdstanr
+                               r-data-table
+                               r-dplyr
+                               r-fastglm
+                               r-furrr
+                               r-future
+                               r-ggdendro
+                               r-ggnewscale
+                               r-ggplot2
+                               r-loo
+                               r-mass
+                               r-patchwork
+                               r-phylogram
+                               r-posterior
+                               r-progressr
+                               r-purrr
+                               r-r-utils
+                               r-stringr
+                               r-tibble
+                               r-tidyselect))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/biobakery/anpan")
+      (synopsis "Quantifying microbial strain-host associations")
+      (description
+       "The goal of anpan is to consolidate statistical methods for strain analysis.
+This includes automated filtering of metagenomic functional profiles, testing genetic
+elements for association with outcomes, phylogenetic association testing, and
+pathway-level random effects models.")
+      (license license:expat))))
+
 (define-public r-bedtorch
   (let ((commit "f5ff4f83b94f59eac660333c64e4b2f296b35cea")
         (revision "1"))

base-commit: c551e406a75273583ae3fef92f32468f905cc07f
prerequisite-patch-id: 70095eccc2035390725bf119749d138d609d2b83
prerequisite-patch-id: 016f9a35b1da6b5916599f4cc6616fc9738c2b46
-- 
2.34.1

Message #10 received at 71651-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 71651-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-anpan.
Date: Mon, 01 Jul 2024 15:49:55 +0200

Applied, thank you!

-- 
Ricardo

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