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| author | Ricardo Wurmus <rekado@elephly.net> | 2021-02-19 23:30:28 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-02-19 23:35:04 +0100 |
| commit | f310b06685cb9b1f95150b24f3eed82ca280c1d2 (patch) | |
| tree | 80578a4839e22e665295a749bb731839797318d1 /gnu | |
| parent | 96193caaa14e575cc2917d0fd7ca8c7499109635 (diff) | |
| download | guix-f310b06685cb9b1f95150b24f3eed82ca280c1d2.tar.gz | |
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.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 22 |
1 files changed, 14 insertions, 8 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7d5521e91d..c8ddf8e3d7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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) |