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gnu: nanopolish: Fix script wrapping.

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* gnu/packages/bioinformatics.scm (nanopolish)[arguments]: Fix wrap-programs
phase.
[inputs]: Add Guile for wrap-script; add bioperl and perl-getopt-long for Perl
scripts.
This commit is contained in:
Ricardo Wurmus 2021-02-19 23:30:28 +01:00
parent 96193caaa1
commit f310b06685
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1 changed files with 14 additions and 8 deletions
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gnu/packages/bioinformatics.scm
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@ -14249,18 +14249,24 @@ choosing which reads pass the filter.")
#t)))
(add-after 'install 'wrap-programs
(lambda* (#:key outputs #:allow-other-keys)
(for-each (lambda (file)
(wrap-program file `("PYTHONPATH" ":" prefix (,path))))
(find-files "/share/nanopolish/scripts" "\\.py"))
(for-each (lambda (file)
(wrap-program file `("PERL5LIB" ":" prefix (,path))))
(find-files "/share/nanopolish/scripts" "\\.pl"))
#t)))))
(let ((pythonpath (getenv "PYTHONPATH"))
(perl5lib (getenv "PERL5LIB"))
(scripts (string-append (assoc-ref outputs "out")
"/share/nanopolish/scripts")))
(for-each (lambda (file)
(wrap-program file `("PYTHONPATH" ":" prefix (,pythonpath))))
(find-files scripts "\\.py"))
(for-each (lambda (file)
(wrap-script file `("PERL5LIB" ":" prefix (,perl5lib))))
(find-files scripts "\\.pl"))))))))
(inputs
`(("eigen" ,eigen)
`(("guile" ,guile-3.0) ; for wrappers
("eigen" ,eigen)
("hdf5" ,hdf5)
("htslib" ,htslib)
("perl" ,perl)
("bioperl" ,bioperl-minimal)
("perl-getopt-long" ,perl-getopt-long)
("python" ,python-wrapper)
("python-biopython" ,python-biopython)
("python-numpy" ,python-numpy)