23/163: gnu: find-circ: Wrap with the new Guix PYTHONPATH.

[guix-commits]

apteryx pushed a commit to branch cu/farewell-to-pythonpath
in repository guix.

commit 7c1743b309d9d0929d7d4b478cb8f982a8f19288
Author: Maxim Cournoyer <maxim.cournoyer@gmail.com>
AuthorDate: Fri Jan 22 16:29:58 2021 -0500

    gnu: find-circ: Wrap with the new Guix PYTHONPATH.
    
    * gnu/packages/bioinformatics.scm (find-circ): Delete trailing #t.
    Import the (guix build python-build-system) module.
    [phases]{install}: Wrap with the new Guix PYTHONPATH.
---
 gnu/packages/bioinformatics.scm | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 720d32d..1d2e0ef 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12873,27 +12873,32 @@ conversions, region filtering, FASTA sequence 
extraction and more.")
            "0p77pbqbclqr4srms34y1b9b4njybfpjiknc11ki84f3p8skb3cg"))))
       (build-system gnu-build-system)
       (arguments
-       `(#:tests? #f                    ; there are none
+       `(#:imported-modules ,(cons '(guix build python-build-system)
+                                   %gnu-build-system-modules)
+         #:modules ((guix build gnu-build-system)
+                    ((guix build python-build-system) #:select 
(guix-pythonpath))
+                    (guix build utils))
+         #:tests? #f                    ; there are none
          #:phases
          ;; There is no actual build system.
          (modify-phases %standard-phases
            (delete 'configure)
            (delete 'build)
            (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
+             (lambda* (#:key inputs outputs #:allow-other-keys)
                (let* ((out (assoc-ref outputs "out"))
                       (bin (string-append out "/bin"))
-                      (path (getenv "PYTHONPATH")))
+                      (pythonpath (guix-pythonpath inputs)))
                  (for-each (lambda (script)
                              (install-file script bin)
                              (wrap-program (string-append bin "/" script)
-                               `("PYTHONPATH" ":" prefix (,path))))
+                               `(,pythonpath ":" prefix
+                                             (,(getenv pythonpath)))))
                            '("cmp_bed.py"
                              "find_circ.py"
                              "maxlength.py"
                              "merge_bed.py"
-                             "unmapped2anchors.py")))
-               #t)))))
+                             "unmapped2anchors.py"))))))))
       (inputs
        `(("python2" ,python-2)
          ("python2-pysam" ,python2-pysam)