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gnu: pigx-rnaseq: Fix build.

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* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'patch-knitr.
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Ricardo Wurmus 2022-06-01 10:45:23 +02:00
parent 1600d5cd3a
commit 0c26c8da9d
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gnu/packages/bioinformatics.scm
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@ -10455,6 +10455,13 @@ (define-public pigx-rnaseq
`(#:parallel-tests? #f ; not supported `(#:parallel-tests? #f ; not supported
#:phases #:phases
(modify-phases %standard-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 ;; "test.sh" runs the whole pipeline, which takes a long time and
;; might fail due to OOM. The MultiQC is also resource intensive. ;; might fail due to OOM. The MultiQC is also resource intensive.
(add-after 'unpack 'disable-resource-intensive-test (add-after 'unpack 'disable-resource-intensive-test