bug#57413: closed ([PATCH] gnu: snakemake-7: Fix cluster execution bug)

[GNU bug Tracking System]

Your message dated Mon, 29 Aug 2022 18:10:11 +0200
with message-id <87v8qbc9p8.fsf@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.

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57413: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=57413
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> --- Begin Message ---
>
>
>
> 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
>
>
>
> --- End Message ---

--- Begin Message --- Subject: Re: [bug#57413] [PATCH] gnu: snakemake-7: Fix cluster execution bug Date: Mon, 29 Aug 2022 18:10:11 +0200

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

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

Applied, thanks!

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