From unknown Sat Aug 16 16:11:21 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#57413] [PATCH] gnu: snakemake-7: Fix cluster execution bug Resent-From: Konrad Hinsen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 25 Aug 2022 18:19:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 57413 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 57413@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.166145149330665 (code B ref -1); Thu, 25 Aug 2022 18:19:02 +0000 Received: (at submit) by debbugs.gnu.org; 25 Aug 2022 18:18:13 +0000 Received: from localhost ([127.0.0.1]:51240 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oRHQi-0007yW-Lf for submit@debbugs.gnu.org; Thu, 25 Aug 2022 14:18:12 -0400 Received: from lists.gnu.org ([209.51.188.17]:33644) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oRHQf-0007yO-S4 for submit@debbugs.gnu.org; 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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 Content-Type: text/plain 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-Spam-Score: 0.2 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) * 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 From unknown Sat Aug 16 16:11:21 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Konrad Hinsen Subject: bug#57413: closed (Re: [bug#57413] [PATCH] gnu: snakemake-7: Fix cluster execution bug) Message-ID: References: <87v8qbc9p8.fsf@gnu.org> X-Gnu-PR-Message: they-closed 57413 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 57413@debbugs.gnu.org Date: Mon, 29 Aug 2022 16:11:03 +0000 Content-Type: multipart/mixed; boundary="----------=_1661789463-27717-1" This is a multi-part message in MIME format... ------------=_1661789463-27717-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #57413: [PATCH] gnu: snakemake-7: Fix cluster execution bug which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 57413@debbugs.gnu.org. --=20 57413: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D57413 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1661789463-27717-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 57413-done) by debbugs.gnu.org; 29 Aug 2022 16:10:48 +0000 Received: from localhost ([127.0.0.1]:33610 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oShLc-0007CL-0R for submit@debbugs.gnu.org; Mon, 29 Aug 2022 12:10:48 -0400 Received: from eggs.gnu.org ([209.51.188.92]:53888) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oShLY-0007Bu-GO for 57413-done@debbugs.gnu.org; Mon, 29 Aug 2022 12:10:44 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:45496) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oShLS-0000zT-7h; Mon, 29 Aug 2022 12:10:38 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:Date:References:In-Reply-To:Subject:To: From; bh=QrnJd/BWAkAvXvWSpWjW+d6L1m9yMs6+duK+Tot6Z7s=; b=VfIcHf3DhOQGYhLh/LxL beOD6umSR75SwX+Lxb44RUf9qFkjKag7eeBbjZsC/nNWP/teChYaoPBMLSq5jXzzKjdprA+5+eOsR gUW7aQMbJ7AcQd6EH6s6yIz0wKQ5GXlqYBlL+Zpmu649DSWynvyQOy6icEPhYYMBPQSrsvH5h9NIU JjgJMQBWpyLwErQTIDxCmJlddBKFd42KLx/27fN+KF0QJnDdaGxlZNkV+rmmiPD2/PbhyG1aNc2FO eqlw0fiPGvxeHDTnT1BuLSMZA96K4mF+UEQQYWghZNe1au7WkMS1eGhz8Jlbbs7fvEO1q8JFDS3Yn QvzluKajNu28eQ==; Received: from [84.214.173.6] (port=36060 helo=localhost) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oShL3-0005Hs-ND; Mon, 29 Aug 2022 12:10:16 -0400 From: Marius Bakke To: Konrad Hinsen , 57413-done@debbugs.gnu.org Subject: Re: [bug#57413] [PATCH] gnu: snakemake-7: Fix cluster execution bug In-Reply-To: References: Date: Mon, 29 Aug 2022 18:10:11 +0200 Message-ID: <87v8qbc9p8.fsf@gnu.org> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 57413-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --=-=-= Content-Type: text/plain Konrad Hinsen skriver: > * gnu/packages/python-xyz.scm (snakemake-7): Revise the patch for > the cluster execution script Applied, thanks! --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iIUEARYKAC0WIQRNTknu3zbaMQ2ddzTocYulkRQQdwUCYwzk4w8cbWFyaXVzQGdu dS5vcmcACgkQ6HGLpZEUEHc0tgEA0M7sx+nkG+dq+W1da+/FZ6/jfpdRlzaQNjAX ctzRFioA/07lBiHme7UFFlY6VkV0Tm9vV8BmFzdL+zu9UwMp2ssE =JaOC -----END PGP SIGNATURE----- --=-=-=-- ------------=_1661789463-27717-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 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Thu, 25 Aug 2022 14:17:59 -0400 (EDT) From: Konrad Hinsen To: guix-patches@gnu.org Subject: [PATCH] gnu: snakemake-7: Fix cluster execution bug Date: Thu, 25 Aug 2022 20:17:55 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain 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-Spam-Score: 0.2 (/) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) * 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 ------------=_1661789463-27717-1--