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The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: The execution of Snakemake workflows fails on a cluster because the script that Snakemake executes remotely does not reference Python correctly. This is due to a patch applied in the Guix package definition (build phase call-wrapper-not-wrapped-snakemake, https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages/python-xyz.scm#n9713) which [...] Content analysis details: (1.6 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 0.0 FREEMAIL_FROM Sender email is commonly abused enduser mail provider (konrad.hinsen[at]fastmail.net) 0.0 T_SPF_TEMPERROR SPF: test of record failed (temperror) -0.0 SPF_HELO_PASS SPF: HELO matches SPF record 1.5 SPOOFED_FREEMAIL No description available. 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: -3.3 (---) The execution of Snakemake workflows fails on a cluster because the script that Snakemake executes remotely does not reference Python correctly. This is due to a patch applied in the Guix package definition (build phase call-wrapper-not-wrapped-snakemake, https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages/python-xyz.scm#n9713) which is outdated. The corresponding code in Snakemake was changed significantly in the following commit: https://github.com/snakemake/snakemake/commit/e87cc979bea0567e1cd97722d385f472857df83c#diff-438f3317205fd7130727d0589d2fc1a6c2e1f6fc48c2c04d354a8a09b91ba2f4 Cheers, Konrad From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 25 11:35:15 2022 Received: (at 57136) by debbugs.gnu.org; 25 Aug 2022 15:35:15 +0000 Received: from localhost ([127.0.0.1]:51094 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oREt0-0001Xt-Nb for submit@debbugs.gnu.org; Thu, 25 Aug 2022 11:35:15 -0400 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]:27140) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oRAoV-000075-Vv for 57136@debbugs.gnu.org; Thu, 25 Aug 2022 07:14:21 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=inria.fr; s=dc; h=message-id:date:mime-version:to:from:subject: content-transfer-encoding; bh=FN6+xhVQKxzjLjBiJ5Imm3zlAzB9bWV7TOGx2HjObog=; b=uPYtMITgdoWNDpFcd5aPw7f7Y+RzePRYfnIQM7zuBoAMn8JSxQu0j0xB ObsM595GP3jpOSNP+C6jl/gkN2TBKV2Q1LZq+k9ymVyIeiUxNuT9JRO/N /Z7WktUtqO4phk8e3A+gRmlwMvsYWAr7Pne3tlpJG5hvgyNugisKRXwDk A=; Authentication-Results: mail2-relais-roc.national.inria.fr; dkim=none (message not signed) header.i=none; spf=SoftFail smtp.mailfrom=matthieu.simonin@inria.fr; dmarc=fail (p=none dis=none) d=inria.fr X-IronPort-AV: E=Sophos;i="5.93,262,1654552800"; d="scan'208";a="49954949" Received: from talouette.irisa.fr (HELO [131.254.18.234]) ([131.254.18.234]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 25 Aug 2022 13:14:13 +0200 Message-ID: Date: Thu, 25 Aug 2022 13:14:13 +0200 MIME-Version: 1.0 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:91.0) Gecko/20100101 Thunderbird/91.12.0 Content-Language: en-US To: 57136@debbugs.gnu.org From: Matthieu Simonin Subject: Snakemake cannot execute remote jobs Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 57136 X-Mailman-Approved-At: Thu, 25 Aug 2022 11:35:14 -0400 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 (---) Hi there, I've taken a stab at using it and restoring the patch as Konrad pointed seems the way to go. But I also found that the package definition doesn't follow the guidelines[1] regarding the inputs definition. One should use `propagated-inputs` instead of `inputs` for a python package. In the current situation we can't invoke `snakemake` as a module: `python -m snakemake` fails as the input dependencies aren't linked in the guix profile. This way of invoking snakemake is used internally by snakemake here and there (for instance when calling the unit tests generated by `snakemake --generate-unit-tests`[2][3]. [1]: https://guix.gnu.org/manual/en/html_node/package-Reference.html [2]: https://snakemake.readthedocs.io/en/stable/snakefiles/testing.html [3]: https://github.com/snakemake/snakemake/blob/v7.7.0/snakemake/unit_tests/templates/ruletest.py.jinja2 From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 25 14:26:48 2022 Received: (at 57136) by debbugs.gnu.org; 25 Aug 2022 18:26:48 +0000 Received: from localhost ([127.0.0.1]:51254 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oRHZ2-0008EN-3j for submit@debbugs.gnu.org; Thu, 25 Aug 2022 14:26:48 -0400 Received: from out1-smtp.messagingengine.com ([66.111.4.25]:44403) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oRHYz-0008E9-LU for 57136@debbugs.gnu.org; Thu, 25 Aug 2022 14:26:46 -0400 Received: from compute5.internal (compute5.nyi.internal [10.202.2.45]) by mailout.nyi.internal (Postfix) with ESMTP id A742D5C00B0; Thu, 25 Aug 2022 14:26:39 -0400 (EDT) Received: from mailfrontend1 ([10.202.2.162]) by compute5.internal (MEProxy); Thu, 25 Aug 2022 14:26:39 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=fastmail.net; h= cc:content-type:date:date:from:from:in-reply-to:in-reply-to :message-id:mime-version:references:reply-to:sender:subject :subject:to:to; s=fm1; t=1661451999; x=1661538399; bh=hBC8J/k42k jtpF87JmobrLg/eurRztPvHx1XbMuJvVA=; b=U9MxyZ3pDZT6X1QACNUfbydIFW C2H4YKfp776tbWFwUq1zjAFxLVt2cmt3LL+rOiB1x3j9ow7I8c8S2O6T9F0R1Xyj Rz8lwJgRwvQ6BO+5uuzNVHShhQXW6H71u4/rrS6f5o/2kbl5oYza6SnzrUV/ucSK VSj99NuDtTl4AmYY8bDHyQHnBHhSmfQZnCFChH/VzE6mEO2cZnb7c4O3eoLy8PMV PEql0NybYpONAIVdFV4PLgGAcgs3JyxHIPfMPWUb4MBiyGXUXjer/H1ylZVwL3jw EEvjUDW5ARKc1j6jCS8vHXkJKg/WpN0V5MnDENwQAhlmgWp4G3u7EP/0vfKw== DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-type:date:date:feedback-id :feedback-id:from:from:in-reply-to:in-reply-to:message-id :mime-version:references:reply-to:sender:subject:subject:to:to :x-me-proxy:x-me-proxy:x-me-sender:x-me-sender:x-sasl-enc; s= fm1; t=1661451999; x=1661538399; bh=hBC8J/k42kjtpF87JmobrLg/eurR ztPvHx1XbMuJvVA=; b=Sq8VLxbHzO/OzBzIoZFxES+bZiNvBJiXrx2TVNiJx0aZ xLpdnWnuuTYPfs4kqqPbv5rooLlab9vcXjtPpflKmRLwDgU5NwM6uEupApQfE0Ro w3OC9sHFh+ivZGfaSvBlp5gJ72C3nNkfTMN3HAytnsNyRjoRbn5EosJBPAJbBvwx 82IqKC8Kwh1xN6WwJQX8qrwS5yA2iBIqjNntYnJJDRXQ3dDct76mza7tbDTdgKDb f+guoysfsNsn+wcfYd7ZKBwHtv/EGUX/de9t7BMKU5Mg2msoD4FEXavJH6zvX+ju 8ouFyv1nd4H0E/cORuKXla2iZ6Nve/UFRlVOWacumw== X-ME-Sender: X-ME-Received: X-ME-Proxy-Cause: gggruggvucftvghtrhhoucdtuddrgedvfedrvdejfedguddvfecutefuodetggdotefrod ftvfcurfhrohhfihhlvgemucfhrghsthforghilhdpqfgfvfdpuffrtefokffrpgfnqfgh necuuegrihhlohhuthemuceftddtnecunecujfgurhephffvufgjfhffkfggtgesthdtre dttddttdenucfhrhhomhepmfhonhhrrgguucfjihhnshgvnhcuoehkohhnrhgrugdrhhhi nhhsvghnsehfrghsthhmrghilhdrnhgvtheqnecuggftrfgrthhtvghrnhepgeelleffud euieegteduiefftdelueekleegieeifedtvdeugeeujedvfeejgeehnecuffhomhgrihhn pehgnhhurdhorhhgnecuvehluhhsthgvrhfuihiivgeptdenucfrrghrrghmpehmrghilh hfrhhomhepkhhonhhrrggurdhhihhnshgvnhesfhgrshhtmhgrihhlrdhnvght X-ME-Proxy: Feedback-ID: i184641e2:Fastmail Received: by mail.messagingengine.com (Postfix) with ESMTPA; Thu, 25 Aug 2022 14:26:37 -0400 (EDT) From: Konrad Hinsen To: 57136@debbugs.gnu.org Subject: Re: Snakemake cannot execute remote jobs In-Reply-To: References: Date: Thu, 25 Aug 2022 20:26:36 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 57136 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: -1.7 (-) I have submitted a patch that fixes this problem: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=57413 This is the patch that Matthieu referred to, and which he tested in a cluster environment. 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Thu, 25 Aug 2022 14:50:14 -0400 (EDT) From: Konrad Hinsen To: 57136@debbugs.gnu.org Subject: Re: Snakemake cannot execute remote jobs In-Reply-To: References: Date: Thu, 25 Aug 2022 20:50:12 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 57136 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: -1.7 (-) The other problem that Matthieu pointed out (but which is unrelated to the initial bug report) is fixed by the following two patches for snakemake-6 and snakemake-7: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=57414 https://debbugs.gnu.org/cgi/bugreport.cgi?bug=57415 Cheers, Konrad From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 29 12:50:51 2022 Received: (at 57136-done) by debbugs.gnu.org; 29 Aug 2022 16:50:51 +0000 Received: from localhost ([127.0.0.1]:33719 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oShyM-0008Jt-S9 for submit@debbugs.gnu.org; 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Mon, 29 Aug 2022 12:50:42 -0400 (EDT) From: Konrad Hinsen To: 57136-done@debbugs.gnu.org Subject: Re: Snakemake cannot execute remote jobs Date: Mon, 29 Aug 2022 18:50:41 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 57136-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: -1.7 (-) The bug is fixed via the patch referenced above in commit 5831155175614726685edab7efa60ce48e4da1f5. From unknown Sun Jun 15 08:55:41 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Tue, 27 Sep 2022 11:24:05 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator