From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp10.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms5.migadu.com with LMTPS id IGe1MarA9GJ/+wAAbAwnHQ (envelope-from ) for ; Thu, 11 Aug 2022 10:41:14 +0200 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp10.migadu.com with LMTPS id UOi5MKrA9GIvbgEAG6o9tA (envelope-from ) for ; Thu, 11 Aug 2022 10:41:14 +0200 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id DC8FF29461 for ; Thu, 11 Aug 2022 10:41:12 +0200 (CEST) Received: from localhost ([::1]:55454 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1oM3kc-0000a8-Ml for larch@yhetil.org; Thu, 11 Aug 2022 04:41:10 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:36648) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oM3kW-0000Zm-7u for bug-guix@gnu.org; Thu, 11 Aug 2022 04:41:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:33487) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1oM3kV-0004hm-DT for bug-guix@gnu.org; Thu, 11 Aug 2022 04:41:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1oM3kU-0002Ip-93 for bug-guix@gnu.org; Thu, 11 Aug 2022 04:41:02 -0400 X-Loop: help-debbugs@gnu.org Subject: bug#57136: Snakemake cannot execute remote jobs Resent-From: Konrad Hinsen Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Thu, 11 Aug 2022 08:41:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 57136 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 57136@debbugs.gnu.org X-Debbugs-Original-To: bug-guix@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.16602072388796 (code B ref -1); Thu, 11 Aug 2022 08:41:02 +0000 Received: (at submit) by debbugs.gnu.org; 11 Aug 2022 08:40:38 +0000 Received: from localhost ([127.0.0.1]:51467 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oM3k2-0002He-Gi for submit@debbugs.gnu.org; Thu, 11 Aug 2022 04:40:38 -0400 Received: from lists.gnu.org ([209.51.188.17]:42650) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oM3jp-0002HF-Rw for submit@debbugs.gnu.org; Thu, 11 Aug 2022 04:40:33 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:36492) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oM3jp-0000QQ-MS for bug-guix@gnu.org; Thu, 11 Aug 2022 04:40:21 -0400 Received: from wout1-smtp.messagingengine.com ([64.147.123.24]:49201) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oM3jb-0004RN-8i for bug-guix@gnu.org; Thu, 11 Aug 2022 04:40:21 -0400 Received: from compute2.internal (compute2.nyi.internal [10.202.2.46]) by mailout.west.internal (Postfix) with ESMTP id C80393200944; Thu, 11 Aug 2022 04:40:00 -0400 (EDT) Received: from mailfrontend1 ([10.202.2.162]) by compute2.internal (MEProxy); Thu, 11 Aug 2022 04:40:01 -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:message-id :mime-version:reply-to:sender:subject:subject:to:to; s=fm1; t= 1660207200; x=1660293600; bh=l7vsgVcYXGiMqz1lcrSAx3oktbUcxT23Unp Z6cI4E2Y=; b=rPCwIjswrs2Cb2vADp+ob+nw1+mCyQgrJKH9T8GVAuew0CZJZsH ZntEBzRLSqdO2Wt4zxUBEvDg9gNuECI0yfXkpWpbpgeJt7DT06wugXMkCVkw2+Y5 /QIaIfQ3Bo871zf1FZam2wzI7YfBs4fBojcfR7U+oCq00Voxyup1mqTbGhzGIh9i iqToCgPcrFBi6KSU2Xi1i0oVablLtkeMY7bXzr0XV0Y1r8mWVy25cmfi/i70k/Z6 kNtbyp3WaYUcFtoimnp1SKCmIqKou2BqMDpRa3eXdF0tEXAmRrqXhhR/RXgcjSg5 7OIB45X3SnrwUyjy07j67LWwBbKv8VkSSOQ== 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:message-id:mime-version :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=1660207200; x= 1660293600; bh=l7vsgVcYXGiMqz1lcrSAx3oktbUcxT23UnpZ6cI4E2Y=; b=x Pndk5VlznCdzss740BE9sgRdAgRd4t5Xaijd2gGcQR4S04+kExPR3v9EW1rbje+h QKgszinADfgE39xShOkFCv+6BiyZDyWWjkQ3cNVkBvLMxoU2/RNFaBPfWu42JfQ3 SoKLTWJNDXHEkCgN/j1tslOvsoukXjX0NQRSArpS5rJ4Znx02igcrXSx5623I6ZJ RpdfOFVPX6DtjyFPyfzjv36TiZ0MiXgrz1JzneQJyr0JuMdqPx3EOgR3rp3inU5u 2NINvwyQgGy0GWBOJzDChl9RaF1adVRL3oKZYK7wRpx/aVBLfDArEk+m/rV0j9te UTKfno/Uo++h6vnVoaNJg== X-ME-Sender: X-ME-Received: X-ME-Proxy-Cause: gggruggvucftvghtrhhoucdtuddrgedvfedrvdeggedgtdekucetufdoteggodetrfdotf fvucfrrhhofhhilhgvmecuhfgrshhtofgrihhlpdfqfgfvpdfurfetoffkrfgpnffqhgen uceurghilhhouhhtmecufedttdenucenucfjughrpefhvffufffkgggtsehttdertddttd dtnecuhfhrohhmpefmohhnrhgrugcujfhinhhsvghnuceokhhonhhrrggurdhhihhnshgv nhesfhgrshhtmhgrihhlrdhnvghtqeenucggtffrrghtthgvrhhnpeffgeegieeuhfeihe duteeigedutdeivdevudetgeegffdtvdegleehgeeugefhjeenucffohhmrghinhepghhn uhdrohhrghdpghhithhhuhgsrdgtohhmnecuvehluhhsthgvrhfuihiivgeptdenucfrrg hrrghmpehmrghilhhfrhhomhepkhhonhhrrggurdhhihhnshgvnhesfhgrshhtmhgrihhl rdhnvght X-ME-Proxy: Feedback-ID: i184641e2:Fastmail Received: by mail.messagingengine.com (Postfix) with ESMTPA; Thu, 11 Aug 2022 04:39:59 -0400 (EDT) From: Konrad Hinsen Date: Thu, 11 Aug 2022 10:39:56 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain Received-SPF: pass client-ip=64.147.123.24; envelope-from=konrad.hinsen@fastmail.net; helo=wout1-smtp.messagingengine.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 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, 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: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1660207273; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:mime-version:mime-version: content-type:content-type:resent-cc:resent-from:resent-sender: resent-message-id:list-id:list-help:list-unsubscribe:list-subscribe: list-post:dkim-signature; bh=l7vsgVcYXGiMqz1lcrSAx3oktbUcxT23UnpZ6cI4E2Y=; b=jK54AHNnUBrhmwVkCsJTFWuerJk6IZSg66mWMVEEN0L5h0ZN2yO0tB/YOQHVFPk1vdKiAF XH8RasydrwfGfeqoNeTbMmZEnHbIhoZqmgq1Vn5M1M+Rb/Bfo7GFw4pWoePybPt6mVN9Vk P4zzcRdgsgU4uUoYhdx4RDQT0z3kxVlZJbV0+SqMBkQqazK2hPL8v/vH1QFuuyrcX7JRv9 bGc/xZj02xbDQdTO0nMmopjCp9XXp3sTgH4QFJTcigLSh6h079rI0lGiW0IumKMFs6TGFX U3gABbIdcqRf5hu9bqbJ3l/LV8EBCCHPCB2BV9n/Okkpm59f3M8U8NhF7+0Cnw== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1660207273; a=rsa-sha256; cv=none; b=gdf7a3lYTtH0FeyQCaXDE8/04uPjbkhFTBTS9PWYQhTWqv7kRECP5ehqU+j2MUdr+J7kTA LmjQYc5voGP92r4S/ci4mYjZUnYff1PAPWvEUGh5xj5YlaygOGbWqFZ9C/cJg+MpFC2ScU p8RTLBqzUtyVoQQk6YZUsExOBFUTY7+14CoKB0xHK2UaaqrfT5t6VaLcGTqqSkYvLKitAo zXp/xEIFVUIoK44a3HyIZI8VwLVoX15nZ6AElzqDRRwUF/jSbk8MlNqxZl4eWCl7CcXa9V 6F3b1p6PGtHMPH4IVsYkvLZn/3bq+ftNxd24UtzJGpKI2wBnW8cIoLEjjn6YyA== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=fastmail.net header.s=fm1 header.b=rPCwIjsw; dkim=fail ("headers rsa verify failed") header.d=messagingengine.com header.s=fm1 header.b="x Pndk5V"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=fastmail.net (policy=none); spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 5.42 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=fastmail.net header.s=fm1 header.b=rPCwIjsw; dkim=fail ("headers rsa verify failed") header.d=messagingengine.com header.s=fm1 header.b="x Pndk5V"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=fastmail.net (policy=none); spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: DC8FF29461 X-Spam-Score: 5.42 X-Migadu-Scanner: scn0.migadu.com X-TUID: ci6sBlKT1xK+ 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