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01/02: gnu: pigx-rnaseq: Fix build.
From: |
guix-commits |
Subject: |
01/02: gnu: pigx-rnaseq: Fix build. |
Date: |
Wed, 1 Jun 2022 04:47:26 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit 0c26c8da9d9bb86bfbe8fe9a52ba7b2ba9c6e3ec
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Wed Jun 1 10:45:23 2022 +0200
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