02/02: gnu: nanopolish: Fix script wrapping.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit f310b06685cb9b1f95150b24f3eed82ca280c1d2
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri Feb 19 23:30:28 2021 +0100

    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.
---
 gnu/packages/bioinformatics.scm | 22 ++++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7d5521e..c8ddf8e 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)