From patchwork Mon Mar 11 18:22:42 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 61676 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id A200627BBE9; Mon, 11 Mar 2024 18:28:41 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id B41F727BBE2 for ; Mon, 11 Mar 2024 18:28:38 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rjkKF-0005Ru-Oi; Mon, 11 Mar 2024 14:24:41 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1rjkK8-0005IQ-7n for guix-patches@gnu.org; Mon, 11 Mar 2024 14:24:33 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rjkK5-00082u-1G for guix-patches@gnu.org; Mon, 11 Mar 2024 14:24:31 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rjkKc-00044T-HW; Mon, 11 Mar 2024 14:25:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH 7/7] gnu: Add python-toil. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, guix-patches@gnu.org Resent-Date: Mon, 11 Mar 2024 18:25:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac X-Debbugs-Original-Xcc: Arun Isaac Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.171018144515557 (code B ref 69736); Mon, 11 Mar 2024 18:25:02 +0000 Received: (at 69736) by debbugs.gnu.org; 11 Mar 2024 18:24:05 +0000 Received: from localhost ([127.0.0.1]:41277 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJg-00042g-DW for submit@debbugs.gnu.org; Mon, 11 Mar 2024 14:24:05 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:45078) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJd-00041S-KN for 69736@debbugs.gnu.org; Mon, 11 Mar 2024 14:24:02 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:MIME-Version: References:In-Reply-To:Message-ID:Date:Subject:Cc:To:From:Sender:Reply-To: Content-Type:Content-ID:Content-Description:Resent-Date:Resent-From: Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id:List-Help: List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=z4KAC93+/1ABRdlZv+/tyF8t1945i7GAv+35cqOAJ1Y=; b=NYk1kvxaQRQwD4tchHH8LuuurQ skqFKkcwVElQjoEKK7zXdsth9rR4INQ2cxFboKrxGaLzZVCbc1LMW7Y2QIdeQi2sX+qDimZAq5sGr R8P6wK/shJVhumO/GnzAnzC/+dyGTsPdU/XVX6CwO2jS9Yk93ZGuE5YkLWj82HYGufhHorhqdqa62 PqwUOWX7ebmYNrc2gruv0fsaGkXtC8npTaqTVvycQ7W1/X4Jh5UC715gHs1sfoN60aebk2+tIqTQB wZxHotgIFpFnq1R1iYANuizTxu9rWAEdk3Wyr2Gaz+fDBooZNJKX0Cu/si1zHg8e7mA0XRfLXqD2m uKEos0yA==; Received: from [192.168.2.1] (port=54074 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96.1) (envelope-from ) id 1rjkHR-0007WI-2Y; Mon, 11 Mar 2024 18:21:46 +0000 From: Arun Isaac Date: Mon, 11 Mar 2024 18:22:42 +0000 Message-ID: <79a9044f3ced28df0b987c383f25b7fb657aac6e.1710180345.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-toil): New variable. Change-Id: I1a6c071eaa9169c1e0cd7c74d1117490ee7bf267 --- gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 68577ded17..aed57796cd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -87,6 +87,7 @@ (define-module (gnu packages bioinformatics) #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) #:use-module (gnu packages dlang) + #:use-module (gnu packages docker) #:use-module (gnu packages file) #:use-module (gnu packages flex) #:use-module (gnu packages gawk) @@ -5338,6 +5339,67 @@ (define-public python-cwltool (modify-inputs (package-inputs cwltool) (delete "node"))))) +(define-public python-toil + (package + (name "python-toil") + (version "6.1.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "toil" version)) + (sha256 + (base32 + "0hwaihnncsfxw0sf3iigvgw6nylrb56lpk8qjadkgazr98dsp4ha")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'disable-optional-features + (lambda _ + (substitute* "requirements-cwl.txt" + ;; Loosen version restrictions on ruamel.yaml. + (("ruamel.yaml[<>=.,[:digit:]]*\n") "ruamel.yaml\n") + ;; Remove optional dependency on galaxy-util and + ;; galaxy-tool-util. TODO: Package these and restore these + ;; dependencies. + (("galaxy-util[^\n]*") "") + (("galaxy-tool-util[^\n]*") "")) + ;; Disable optional wdl, wes and mesos features. We don't yet + ;; have dependencies packaged for them. TODO: Package these + ;; dependencies and enable these features. + (substitute* "setup.py" + (("\"wdl\",") "") + (("toil-cwl-runner = toil.cwl.cwltoil:main \\[cwl\\]") + "toil-cwl-runner = toil.cwl.cwltoil:main") + (("'toil-wdl-runner = toil.wdl.wdltoil:main \\[wdl\\]',") "") + (("'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main \\[server\\]',") "") + (("'_toil_mesos_executor = toil.batchSystems.mesos.executor:main \\[mesos\\]',") ""))))))) + (propagated-inputs + (list python-addict + python-cachecontrol + python-configargparse + python-cwltool + python-dateutil + python-dill + python-docker + python-enlighten + python-psutil + python-pypubsub + python-pytz + python-pyyaml + python-requests + python-ruamel.yaml + python-typing-extensions-4.10 + python-urllib3)) + (home-page "https://github.com/DataBiosphere/toil") + (synopsis "Scalable, efficient and cross-platform workflow engine") + (description "Toil is a scalable, efficient, cross-platform pipeline +management system, written entirely in Python, and designed around the +principles of functional programming.") + (license (list license:asl2.0 ;; main license + license:expat)))) ;; src/toil/batchSystems/lsf.py and + ;; src/toil/batchSystems/lsfHelper.py + (define-public python-dendropy (package (name "python-dendropy")