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Thu, 25 Aug 2022 14:17:59 -0400 (EDT) From: Konrad Hinsen Date: Thu, 25 Aug 2022 20:17:55 +0200 Message-ID: MIME-Version: 1.0 Received-SPF: pass client-ip=66.111.4.25; envelope-from=konrad.hinsen@fastmail.net; helo=out1-smtp.messagingengine.com X-Spam_score_int: -27 X-Spam_score: -2.8 X-Spam_bar: -- X-Spam_report: (-2.8 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_LOW=-0.7, RCVD_IN_MSPIKE_H3=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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?