GNU bug report logs - #57413
[PATCH] gnu: snakemake-7: Fix cluster execution bug

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Marius Bakke <marius <at> gnu.org>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#57413: closed ([PATCH] gnu: snakemake-7: Fix cluster
 execution bug)
Date: Mon, 29 Aug 2022 16:11:03 +0000

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Your message dated Mon, 29 Aug 2022 18:10:11 +0200
with message-id <87v8qbc9p8.fsf <at> gnu.org>
and subject line Re: [bug#57413] [PATCH] gnu: snakemake-7: Fix cluster execution bug
has caused the debbugs.gnu.org bug report #57413,
regarding [PATCH] gnu: snakemake-7: Fix cluster execution bug
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


-- 
57413: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=57413
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Konrad Hinsen <konrad.hinsen <at> fastmail.net>
To: guix-patches <at> gnu.org
Subject: [PATCH] gnu: snakemake-7: Fix cluster execution bug
Date: Thu, 25 Aug 2022 20:17:55 +0200

* 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

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From: Marius Bakke <marius <at> gnu.org>
To: Konrad Hinsen <konrad.hinsen <at> fastmail.net>, 57413-done <at> debbugs.gnu.org
Subject: Re: [bug#57413] [PATCH] gnu: snakemake-7: Fix cluster execution bug
Date: Mon, 29 Aug 2022 18:10:11 +0200

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Konrad Hinsen <konrad.hinsen <at> fastmail.net> skriver:

> * gnu/packages/python-xyz.scm (snakemake-7): Revise the patch for
> the cluster execution script

Applied, thanks!

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