From 0c26c8da9d9bb86bfbe8fe9a52ba7b2ba9c6e3ec Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 1 Jun 2022 10:45:23 +0200
Subject: gnu: pigx-rnaseq: Fix build.

* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'patch-knitr.
---
 gnu/packages/bioinformatics.scm | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7059be7d24..6ce011af0f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10455,6 +10455,13 @@ once.  This package provides tools to perform Drop-seq analyses.")
      `(#:parallel-tests? #f             ; not supported
        #:phases
        (modify-phases %standard-phases
+         ;; knitr 0.39 changes the default behavior of how graphics are
+         ;; included.
+         (add-after 'unpack 'patch-knitr
+           (lambda _
+             (substitute* "scripts/runDeseqReport.R"
+               (("outFile <- paste0" m)
+                (string-append "options(knitr.graphics.rel_path = FALSE)\n" m)))))
          ;; "test.sh" runs the whole pipeline, which takes a long time and
          ;; might fail due to OOM.  The MultiQC is also resource intensive.
          (add-after 'unpack 'disable-resource-intensive-test
-- 
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