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gnu: bismark: Fix references to gunzip.

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* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to
gunzip executable.
[inputs]: Add gzip.
This commit is contained in:
Ricardo Wurmus 2018-03-19 20:53:27 +01:00
parent 51237011bf
commit 096589035e
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1 changed files with 10 additions and 1 deletions
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11
gnu/packages/bioinformatics.scm
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@ -11514,7 +11514,7 @@ (define-public bismark
(delete 'configure)
(delete 'build)
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out")
"/bin"))
(docdir (string-append (assoc-ref outputs "out")
@ -11537,7 +11537,16 @@ (define-public bismark
scripts)
(for-each (lambda (file) (install-file file docdir))
docs)
;; Fix references to gunzip
(substitute* (map (lambda (file)
(string-append bin "/" file))
scripts)
(("\"gunzip -c")
(string-append "\"" (assoc-ref inputs "gzip")
"/bin/gunzip -c")))
#t))))))
(inputs
`(("gzip" ,gzip)))
(home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/")
(synopsis "Map bisulfite treated sequence reads and analyze methylation")
(description "Bismark is a program to map bisulfite treated sequencing