From be067c908c90b9d9f798fdf36f744f72c884f3bd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 7 Jun 2021 16:49:12 +0200 Subject: gnu: pigx-rnaseq: Adjust to upgrade of salmon. * gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase "use-latest-salmon". --- gnu/packages/bioinformatics.scm | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a34b123264..206c193952 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10371,6 +10371,13 @@ once. This package provides tools to perform Drop-seq analyses.") `(#:parallel-tests? #f ; not supported #:phases (modify-phases %standard-phases + ;; See https://github.com/BIMSBbioinfo/pigx_rnaseq/issues/96 + (add-after 'unpack 'use-latest-salmon + (lambda _ + (substitute* "snakefile.py" + (("\"sa.bin\"") "\"pos.bin\"")) + (substitute* "tests/test_salmon/test_salmon_index.sh.in" + (("sa.bin") "pos.bin")))) ;; "test.sh" runs STAR, which requires excessive amounts of memory. (add-after 'unpack 'disable-resource-intensive-test (lambda _ -- cgit v1.2.3