gnu: nanopolish: Fix script wrapping.
* 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.
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@ -14249,18 +14249,24 @@ (define-public nanopolish
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#t)))
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#t)))
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(add-after 'install 'wrap-programs
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(add-after 'install 'wrap-programs
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(lambda* (#:key outputs #:allow-other-keys)
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(lambda* (#:key outputs #:allow-other-keys)
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(for-each (lambda (file)
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(let ((pythonpath (getenv "PYTHONPATH"))
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(wrap-program file `("PYTHONPATH" ":" prefix (,path))))
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(perl5lib (getenv "PERL5LIB"))
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(find-files "/share/nanopolish/scripts" "\\.py"))
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(scripts (string-append (assoc-ref outputs "out")
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(for-each (lambda (file)
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"/share/nanopolish/scripts")))
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(wrap-program file `("PERL5LIB" ":" prefix (,path))))
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(for-each (lambda (file)
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(find-files "/share/nanopolish/scripts" "\\.pl"))
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(wrap-program file `("PYTHONPATH" ":" prefix (,pythonpath))))
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#t)))))
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(find-files scripts "\\.py"))
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(for-each (lambda (file)
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(wrap-script file `("PERL5LIB" ":" prefix (,perl5lib))))
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(find-files scripts "\\.pl"))))))))
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(inputs
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(inputs
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`(("eigen" ,eigen)
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`(("guile" ,guile-3.0) ; for wrappers
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("eigen" ,eigen)
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("hdf5" ,hdf5)
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("hdf5" ,hdf5)
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("htslib" ,htslib)
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("htslib" ,htslib)
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("perl" ,perl)
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("perl" ,perl)
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("bioperl" ,bioperl-minimal)
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("perl-getopt-long" ,perl-getopt-long)
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("python" ,python-wrapper)
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("python" ,python-wrapper)
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("python-biopython" ,python-biopython)
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("python-biopython" ,python-biopython)
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("python-numpy" ,python-numpy)
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("python-numpy" ,python-numpy)
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