20/163: gnu: gess: Adjust to use Guix PYTHONPATH.

[guix-commits]

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

commit 55195f00f464b8e6f03f9c74b041690a255a5df2
Author: Maxim Cournoyer <maxim.cournoyer@gmail.com>
AuthorDate: Fri Jan 22 14:04:26 2021 -0500

    gnu: gess: Adjust to use Guix PYTHONPATH.
    
    * gnu/packages/bioinformatics.scm (gess): Import required module and adjust
    the wrapping of the GESS.py so that it uses the newly introduced Guix
    PYTHONPATH environment variable.
---
 gnu/packages/bioinformatics.scm | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 152f104..e9e53f8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10670,7 +10670,12 @@ remove biased methylation positions for RRBS sequence 
files.")
                 "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f                      ; no tests
+     `(#: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                      ; no tests
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
@@ -10678,6 +10683,7 @@ remove biased methylation positions for RRBS sequence 
files.")
          (replace 'install
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((python (assoc-ref inputs "python"))
+                    (pythonpath (guix-pythonpath inputs))
                     (out    (assoc-ref outputs "out"))
                     (bin    (string-append out "/bin/"))
                     (target (string-append
@@ -10699,11 +10705,10 @@ matplotlib.use('Agg')
 " line)))
                ;; Make sure GESS has all modules in its path
                (wrap-script (string-append target "GESS.py")
-                 `("PYTHONPATH" ":" = (,target ,(getenv "PYTHONPATH"))))
+                 `(,pythonpath ":" = (,target ,(getenv pythonpath))))
                (mkdir-p bin)
                (symlink (string-append target "GESS.py")
-                        (string-append bin "GESS.py"))
-               #t))))))
+                        (string-append bin "GESS.py"))))))))
     (inputs
      `(("python" ,python-2)
        ("python2-pysam" ,python2-pysam)