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gnu: pigx-rnaseq: Adjust to upgrade of salmon.

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* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase
"use-latest-salmon".
This commit is contained in:
Ricardo Wurmus 2021-06-07 16:49:12 +02:00
parent bb38287570
commit be067c908c
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gnu/packages/bioinformatics.scm
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@ -10371,6 +10371,13 @@ (define-public pigx-rnaseq
`(#:parallel-tests? #f ; not supported `(#:parallel-tests? #f ; not supported
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
;; 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. ;; "test.sh" runs STAR, which requires excessive amounts of memory.
(add-after 'unpack 'disable-resource-intensive-test (add-after 'unpack 'disable-resource-intensive-test
(lambda _ (lambda _