From: Konrad Hinsen <konrad.hinsen@fastmail.net>
To: 57413@debbugs.gnu.org
Subject: [bug#57413] [PATCH] gnu: snakemake-7: Fix cluster execution bug
Date: Thu, 25 Aug 2022 20:17:55 +0200 [thread overview]
Message-ID: <m1r114far0.fsf@fastmail.net> (raw)
* gnu/packages/python-xyz.scm (snakemake-7): Revise the patch for
the cluster execution script
---
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 f7971b75fa..cb3eba77aa 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -9784,15 +9784,14 @@ (define-public snakemake-7
;; 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?
--
2.37.1
next reply other threads:[~2022-08-25 18:19 UTC|newest]
Thread overview: 2+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-08-25 18:17 Konrad Hinsen [this message]
2022-08-29 16:10 ` bug#57413: [PATCH] gnu: snakemake-7: Fix cluster execution bug Marius Bakke
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