mbakke pushed a commit to branch master
in repository guix.
commit 5831155175614726685edab7efa60ce48e4da1f5
Author: Konrad Hinsen <[email protected]>
AuthorDate: Thu Aug 25 20:17:55 2022 +0200
gnu: snakemake-7: Fix cluster execution bug
* gnu/packages/python-xyz.scm (snakemake-7)[arguments]: Revise the patch for
the cluster execution script
Signed-off-by: Marius Bakke <[email protected]>
---
gnu/packages/python-xyz.scm | 11 +++++------
1 file changed, 5 insertions(+), 6 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 30645fc4a0..0accf918ee 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -9739,15 +9739,14 @@ Python style, together with a fast and comfortable
execution environment.")
;; For cluster execution Snakemake will call Python. Since there is
;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We
;; fix this by calling the snakemake wrapper instead.
-
- ;; XXX: There is another instance of sys.executable on line 692, but
- ;; it is not clear how to patch it.
(add-after 'unpack 'call-wrapper-not-wrapped-snakemake
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "snakemake/executors/__init__.py"
- (("\\{sys.executable\\} -m snakemake")
- (string-append (assoc-ref outputs "out")
- "/bin/snakemake")))))
+ (("self\\.get_python_executable\\(\\),")
+ "")
+ (("\"-m snakemake\"")
+ (string-append "\"" (assoc-ref outputs "out")
+ "/bin/snakemake" "\"")))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
