From 1c559a129c0c62fb1a52235965198557695e0790 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 29 Nov 2024 11:50:45 +0100
Subject: [PATCH] gnu: r-rnbeads: Add missing inputs.

* gnu/packages/bioconductor.scm (r-rnbeads)[native-inputs]: Add ghostscript,
r-doparallel, r-impute, r-missmethyl, r-qvalue, r-rnbeads-hg19, and
r-rtracklayer.
[inputs]: Add kentutils.
[source]: Add snippet to delete bundled binaries.
[arguments]: Add phase 'link-to-executables; disable vignettes.
[properties]: Tell updater what inputs to ignore and what to keep.
[description]: Reflow paragraph.

Change-Id: Ied81eeee2210fac43c3868d268aa20c1d0a0fb50
---
 gnu/packages/bioconductor.scm | 42 ++++++++++++++++++++++++++++++-----
 1 file changed, 37 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7f2d81dd41..a85aaf7005 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9822,9 +9822,32 @@ (define-public r-rnbeads
        (method url-fetch)
        (uri (bioconductor-uri "RnBeads" version))
        (sha256
-        (base32 "006kmfg1lysa9z9cbc507l54xh1apslrxxk41w65zp7bqkhs2zj9"))))
-    (properties `((upstream-name . "RnBeads")))
+        (base32 "006kmfg1lysa9z9cbc507l54xh1apslrxxk41w65zp7bqkhs2zj9"))
+       (modules '((guix build utils)))
+       (snippet
+        '(delete-file-recursively "inst/bin"))))
+    (properties
+     `((upstream-name . "RnBeads")
+       (updater-extra-inputs . ("kentutils"))
+       (updater-extra-native-inputs
+        . ("r-impute" "r-missmethyl" "r-doparallel" "r-qvalue" "ghostscript"))))
     (build-system r-build-system)
+    (arguments
+     (list
+      ;; Vignette ‘RnBeads.Rnw’ overwrites the following ‘tangle’ output by
+      ;; vignette ‘RnBeads_Annotations.Rnw’: RnBeads_Annotations.R
+      #:test-types '(list "tests")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'install 'link-to-executables
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((bin (string-append #$output
+                                        "/site-library/RnBeads/bin/linux_x86.64")))
+                (mkdir-p bin)
+                (symlink (search-input-file inputs "/bin/bedToBigBed")
+                         (string-append bin "/bedToBigBed"))
+                (symlink (search-input-file inputs "/bin/bedGraphToBigWig")
+                         (string-append bin "/bedGraphToBigWig"))))))))
     (propagated-inputs
      (list r-biocgenerics
            r-cluster
@@ -9842,12 +9865,21 @@ (define-public r-rnbeads
            r-methylumi
            r-plyr
            r-s4vectors))
-    (native-inputs (list r-runit))
+    (inputs (list kentutils))
+    (native-inputs
+     (list ghostscript
+           r-doparallel
+           r-impute
+           r-missmethyl
+           r-qvalue
+           r-rnbeads-hg19
+           r-rtracklayer
+           r-runit))
     (home-page "https://bioconductor.org/packages/RnBeads")
     (synopsis "RnBeads")
     (description
-     "@code{RnBeads} facilitates comprehensive analysis of various types of DNA
-methylation data at the genome scale.")
+     "@code{RnBeads} facilitates comprehensive analysis of various types of
+DNA methylation data at the genome scale.")
     (license license:gpl3)))
 
 (define-public r-impute