From 7cc00303ec4563bf9444e8708408cdece8873ae2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 26 Nov 2024 11:43:29 +0100
Subject: [PATCH] gnu: r-sgseq: Add missing inputs.

* gnu/packages/bioconductor.scm (r-sgseq)[native-inputs]: Add
r-bsgenome-hsapiens-ucsc-hg19.
[arguments]: Add phase 'delete-bad-tests.

Change-Id: I5ff9e2af754700e5ba70ad7bdd1be5ec952946a3
---
 gnu/packages/bioconductor.scm | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9acf6c3cde..372996019b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -18967,6 +18967,14 @@ alignment tool.")
          "1xchrzd384wzm81vzrcixyzn3mgnd343cp544yvfzfn2vxr4y1ij"))))
     (properties `((upstream-name . "SGSeq")))
     (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'delete-bad-tests
+           (lambda _
+             ;; This test attempts to download a data file.
+             (delete-file "inst/unitTests/test_predictVariantEffects.R"))))))
     (propagated-inputs
      (list r-annotationdbi
            r-biocgenerics
@@ -18983,7 +18991,7 @@ alignment tool.")
            r-s4vectors
            r-summarizedexperiment))
     (native-inputs
-     (list r-knitr r-runit))
+     (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-runit))
     (home-page "https://bioconductor.org/packages/SGSeq/")
     (synopsis "Splice event prediction and quantification from RNA-seq data")
     (description