From patchwork Mon Mar 11 18:22:41 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 61673 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 E810B27BBEA; Mon, 11 Mar 2024 18:26:26 +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=ham 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 9955627BBE9 for ; Mon, 11 Mar 2024 18:26:26 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rjkJA-0001VR-Nz; Mon, 11 Mar 2024 14:23:32 -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 1rjkJ8-0001OI-Hc for guix-patches@gnu.org; Mon, 11 Mar 2024 14:23:30 -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 1rjkJ8-0007ti-8F for guix-patches@gnu.org; Mon, 11 Mar 2024 14:23:30 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rjkJg-00042W-0R; Mon, 11 Mar 2024 14:24:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH 6/7] gnu: Add python-cwltool. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, guix-patches@gnu.org Resent-Date: Mon, 11 Mar 2024 18:24:03 +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=B69736.171018144215491 (code B ref 69736); Mon, 11 Mar 2024 18:24:03 +0000 Received: (at 69736) by debbugs.gnu.org; 11 Mar 2024 18:24:02 +0000 Received: from localhost ([127.0.0.1]:41258 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJe-00041j-31 for submit@debbugs.gnu.org; Mon, 11 Mar 2024 14:24:02 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:45072) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJa-00041C-H2 for 69736@debbugs.gnu.org; Mon, 11 Mar 2024 14:23:59 -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=TtAL5864SRT6DVZpO4QGoMzniRsqiVoxePwwSHnyqCg=; b=Vqp3DxXhJNhBCLVQg8DmibhOaG S4mHkVrrdkLQT2TmBtYkoq2abNDovcmKW2OLFxAZ4HCMMNspvgs8WMbLkPVeaCjvUQhmahg/s40Tz cT1/DrALCOGJlZm/IzRga0i164V5qqDvAswzRFOBOLolJucWUhNRdIwMKNhl0rJxBn3YnyD1v6kgT R+du9cmIoVf7LLX1/QdoOl3S8d3oqE8kP5/Xq3b+2Ans25MRtRjkWlAXg3ySMbDJ1MRlGjyHRIvjg 4fgKUgJWvBRFNmM+duE5j/1QMR8QlikIGLEBh0WXjf3J9ENWsoBecSaAS2LbLpRn1Sw8kMQ2v4zxq MIUFverQ==; 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 1rjkHO-0007WI-29; Mon, 11 Mar 2024 18:21:43 +0000 From: Arun Isaac Date: Mon, 11 Mar 2024 18:22:41 +0000 Message-ID: <14b0eae1181ad4bc93beaabd2aa1f2ad0d0884ae.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-cwltool): New variable. Change-Id: Ic374d4c02b69c4e6c923d1cc17e629d4a3a6221c --- gnu/packages/bioinformatics.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b8ecea013c..68577ded17 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5326,6 +5326,18 @@ (define-public cwltool CWL descriptions.") (license license:asl2.0))) +;; python-toil tightly integrates with cwltool using it as a library. So, +;; create a library version of cwltool where inputs become propagated inputs. +(define-public python-cwltool + (package + (inherit cwltool) + (name "python-cwltool") + (inputs + (list node)) + (propagated-inputs + (modify-inputs (package-inputs cwltool) + (delete "node"))))) + (define-public python-dendropy (package (name "python-dendropy")