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20/163: gnu: gess: Adjust to use Guix PYTHONPATH.
From: |
guix-commits |
Subject: |
20/163: gnu: gess: Adjust to use Guix PYTHONPATH. |
Date: |
Mon, 25 Jan 2021 02:01:19 -0500 (EST) |
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)
- 110/163: gnu: gedit: Wrap with the new Guix PYTHONPATH., (continued)
- 110/163: gnu: gedit: Wrap with the new Guix PYTHONPATH., guix-commits, 2021/01/25
- 109/163: gnu: d-feet: Wrap with the new Guix PYTHONPATH., guix-commits, 2021/01/25
- 77/163: gnu: meson: Update to 0.56.2., guix-commits, 2021/01/25
- 112/163: gnu: gnome-shell: Wrap with the new Guix PYTHONPATH., guix-commits, 2021/01/25
- 106/163: gnu: gtg: Wrap with the new Guix PYTHONPATH., guix-commits, 2021/01/25
- 111/163: gnu: caribou: Wrap with the new Guix PYTHONPATH., guix-commits, 2021/01/25
- 80/163: gnu: gtk-doc: Wrap with the new Guix PYTHONPATH., guix-commits, 2021/01/25
- 119/163: gnu: komikku: Wrap with the new Guix PYTHONPATH., guix-commits, 2021/01/25
- 121/163: gnu: python-pathos: Do not set PYTHONPATH., guix-commits, 2021/01/25
- 126/163: gnu: python-hdf4: Do not set PYTHONPATH., guix-commits, 2021/01/25
- 20/163: gnu: gess: Adjust to use Guix PYTHONPATH.,
guix-commits <=
- 23/163: gnu: find-circ: Wrap with the new Guix PYTHONPATH., guix-commits, 2021/01/25
- 17/163: gnu: bamm: Update following changes to the Python build system., guix-commits, 2021/01/25
- 28/163: gnu: python-cffi: Do not set PYTHONPATH., guix-commits, 2021/01/25
- 46/163: gnu: avogadro: Wrap with the new Guix PYTHONPATH., guix-commits, 2021/01/25
- 33/163: gnu: python-pyhamcrest: Update to 2.0.2., guix-commits, 2021/01/25
- 52/163: gnu: ibus: Wrap with the new Guix PYTHONPATH., guix-commits, 2021/01/25
- 70/163: gnu: solfege: Wrap with the new Guix PYTHONPATH., guix-commits, 2021/01/25
- 101/163: gnu: presentty: Wrap with the new Guix PYTHONPATH., guix-commits, 2021/01/25
- 87/163: gnu: python-fenics-dijitso: Do not alter PYTHONPATH., guix-commits, 2021/01/25
- 96/163: gnu: entangle: Wrap with the new Guix PYTHONPATH., guix-commits, 2021/01/25