diff options
| author | Konrad Hinsen <konrad.hinsen@fastmail.net> | 2022-08-25 20:17:55 +0200 |
|---|---|---|
| committer | Marius Bakke <marius@gnu.org> | 2022-08-29 18:22:58 +0200 |
| commit | 5831155175614726685edab7efa60ce48e4da1f5 (patch) | |
| tree | ca5de9fa00d8f5fdb87de637231c4e1b7dee139f /gnu | |
| parent | 52aa21cc9a15cdbbae1c72b8fd28adeb66791a9b (diff) | |
| download | guix-patches-5831155175614726685edab7efa60ce48e4da1f5.tar guix-patches-5831155175614726685edab7efa60ce48e4da1f5.tar.gz | |
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 <marius@gnu.org>
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 11 |
1 files 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? |