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gnu: bwa-meth: Capture one more reference to "bwa". 

Reported by: Alexander.Blume <Alexander.Blume@mdc-berlin.de>

* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Capture invocation of
"bwa index" to retain reference to "bwa" package.
This commit is contained in:
Ricardo Wurmus 2019-09-05 12:03:38 +02:00
parent 0e8b91dbc4
commit 79c6d8781b
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GPG Key ID: 197A5888235FACAC
1 changed files with 2 additions and 2 deletions
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@ -1767,8 +1767,8 @@ well as many of the command line options.")
(add-after 'unpack 'keep-references-to-bwa (add-after 'unpack 'keep-references-to-bwa
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(substitute* "bwameth.py" (substitute* "bwameth.py"
(("bwa mem") (("bwa (mem|index)" _ command)
(string-append (which "bwa") " mem")) (string-append (which "bwa") " " command))
;; There's an ill-advised check for "samtools" on PATH. ;; There's an ill-advised check for "samtools" on PATH.
(("^checkX.*") "")) (("^checkX.*") ""))
#t))))) #t)))))