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Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, jgart@dismail.de, guix-patches@gnu.org Resent-Date: Wed, 03 Jul 2024 15:08:04 +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 , jgart X-Debbugs-Original-Xcc: Arun Isaac , jgart Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.172001928115744 (code B ref 69736); Wed, 03 Jul 2024 15:08:04 +0000 Received: (at 69736) by debbugs.gnu.org; 3 Jul 2024 15:08:01 +0000 Received: from localhost ([127.0.0.1]:40087 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1aS-00045r-MS for submit@debbugs.gnu.org; Wed, 03 Jul 2024 11:08:01 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:45704) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1aQ-00045c-H5 for 69736@debbugs.gnu.org; Wed, 03 Jul 2024 11:07:59 -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=7eZBYt0f0Y2Fb4QO4SUVKmPTtCUNtZXNfJiyVhC2/RQ=; b=AjA7hoD5AxxqL27RnlAqbGLyGB pRmeUNT/C1BmP8DnwUWbD1UqWcK1vf3guZSSp+AOQw1+6VZ5OS00qj/Y0dLmHKHYNIvTgSbGoSnau Owop0aOaSMsznnWJeyIZBjPwVGJZirK/1WHTTLgbMyjUSGdAxeKQDANWo56qmaErkWy0kjmXYCnHL OSoARWlZ0liUndVndF6cIRhaMwThQz8dXvx1uE2GAXvtVvdn0/X+/a60pTRFdMDnabIJObqWMDowl dUCHHO39K9DdGxAZNlnNGyu0UQp5YZovyRy6LI+XX0yZfvj2x3cpUulJrohhpmPTGk9twRA33N3zh /yAc6+fQ==; Received: from [192.168.2.1] (port=40016 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 1sP1WU-0005KA-1x; Wed, 03 Jul 2024 16:03:55 +0100 From: Arun Isaac Date: Wed, 3 Jul 2024 16:07:22 +0100 Message-ID: X-Mailer: git-send-email 2.45.2 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit 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+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN X-Spam-Score: 4.11 X-Migadu-Queue-Id: DA2DF763EF X-Migadu-Scanner: mx10.migadu.com X-Migadu-Spam-Score: 4.11 X-TUID: gIG8hpG0WCw7 * 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 b83e18ea78..6d15b1a226 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -88,6 +88,7 @@ (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) @@ -5828,6 +5829,67 @@ (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") -- 2.45.2