From unknown Sun Jun 22 17:11:40 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#69134 <69134@debbugs.gnu.org> To: bug#69134 <69134@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add python-ega-download-client. Reply-To: bug#69134 <69134@debbugs.gnu.org> Date: Mon, 23 Jun 2025 00:11:40 +0000 retitle 69134 [PATCH] gnu: Add python-ega-download-client. reassign 69134 guix-patches submitter 69134 nafkhamdc severity 69134 normal tag 69134 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 14 15:29:30 2024 Received: (at submit) by debbugs.gnu.org; 14 Feb 2024 20:29:30 +0000 Received: from localhost ([127.0.0.1]:53231 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raLso-0002gx-1I for submit@debbugs.gnu.org; Wed, 14 Feb 2024 15:29:30 -0500 Received: from lists.gnu.org ([209.51.188.17]:39006) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raLsl-0002gp-4P for submit@debbugs.gnu.org; Wed, 14 Feb 2024 15:29:28 -0500 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 1raLsS-0002iE-Ka for guix-patches@gnu.org; Wed, 14 Feb 2024 15:29:08 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1raLsQ-0002m4-Fx for guix-patches@gnu.org; Wed, 14 Feb 2024 15:29:08 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1707942527; x=1709756928; bh=X2D52rjAEbg/+kh latEajWBJU5aV9vDzIpVt1VmZ5vE=; b=BUwnpUCWaJN8TFczSDSPAvCF93H21Mh ruUdUvr4SoUneO/cO+v5QZ8on7nRH2CY33Lb+UY/tQ1XRXXqV+OewTZBLtkZ0NIy DOseDPgcJEdqKsDU5VD1EhZCmIqrf8YPxRPdYOAk1/xvadIhiFRIheYzLs2PyS1w p/ZWWUWne0/Q= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 1BF411601A9 for ; Wed, 14 Feb 2024 21:28:46 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.2.1258.28; Wed, 14 Feb 2024 21:28:46 +0100 From: nafkhamdc To: Subject: [PATCH] gnu: Add python-ega-download-client. 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Change-Id: I3233774975989f912281ab2e6ec6ad3362cae18b --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bcfe3c2656..863bf1ff26 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2525,6 +2525,43 @@ (define-public python-pybedtools ;; licensed lgpl2.1+ (license (list license:expat license:lgpl2.1+)))) +(define-public python-ega-download-client + (package + (name "python-ega-download-client") + (version "5.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/EGA-archive/ega-download-client") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0k9rfq2yyvfxs5sq9lsm8krp9ddx4s18hv85ikf3b37zv24kpwjk")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags '(list "-k" + ;; These tests fail because they require internet access. + (string-append "not test_download.py" + " and not test_htsget.py" + " and not test_commands.py")) + #:phases '(modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "setup.py" + (("==") + ">="))))))) + (propagated-inputs (list python-htsget python-psutil python-requests + python-tqdm python-urllib3)) + (native-inputs (list python-coverage python-pytest python-pyfakefs + python-responses)) + (home-page "https://github.com/EGA-archive/ega-download-client") + (synopsis "EGA download client: pyEGA3") + (description + "PyEGA3 is a tool for viewing and downloading files from authorized EGA datasets.") + (license license:asl2.0))) + (define-public python-scdamandtools (package (name "python-scdamandtools") base-commit: 2ba2875dbda4b080fcad4e6d672bb4104d59dd0c -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 15 06:01:09 2024 Received: (at 69134-done) by debbugs.gnu.org; 15 Feb 2024 11:01:09 +0000 Received: from localhost ([127.0.0.1]:54173 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raZUK-0004pL-RI for submit@debbugs.gnu.org; Thu, 15 Feb 2024 06:01:09 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21037) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raZUI-0004pD-SC for 69134-done@debbugs.gnu.org; Thu, 15 Feb 2024 06:01:07 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1707994845; cv=none; d=zohomail.com; s=zohoarc; b=Ay7j1PLFgxLOtEJ00QdFeO7XCvCG9JjcJXuu3uRlErMzsr8pTKteLoKUaUmcvLDiqjNIBgBqO0cNMXl+kzPJEniiLaIyJynSrnxAXnH6K1U29SV2ZTTQqfufmdfg0LNl/wQHDXdcY2VmqekAMBXF4HjFPSkWVDLcFYo+//S+aGU= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1707994845; h=Content-Type:Cc:Cc:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To; bh=zXhBRoR1JyoSRykodPx1rNCIFy8rzmpQ/PQbZ624Y7o=; b=OkCeWFHSAZpAFxOMGKdixHaAbRqnQiuR8oRPRpSMoafGlSz4C4/PgDFfbfVGvDhgwxxZAhlOxMzlK09udc1mGhad/hPuY3sUUZeNTTM/2LNywi9UzDBWhSVjem2ZaelCf32bzY+V7inT+FtJ/jttbfg28aUDj3WV5a9Ntb3mWoI= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1707994845; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To; bh=zXhBRoR1JyoSRykodPx1rNCIFy8rzmpQ/PQbZ624Y7o=; b=JFzhOYyh3bvjCL8HdUilQfLRWTzrmrP2b7MynFqHOX0M6Zd/eVR0t8RKNfh5gKBN hoMUbgJb5eDfpcI9lsp5yPZyTeCJMKirrtMH9oeK8ZZRo8kK3lg/V+Om69AQJFfKV+m 94REG7H1dvwmgTHd05tnJXxzVva+okMwTq24OvDw= Received: from localhost (141.80.245.209 [141.80.245.209]) by mx.zohomail.com with SMTPS id 1707994845029831.7438624359078; Thu, 15 Feb 2024 03:00:45 -0800 (PST) User-agent: mu4e 1.10.8; emacs 29.1 From: Ricardo Wurmus To: 69134-done@debbugs.gnu.org Subject: [PATCH] gnu: Add python-ega-download-client. Date: Thu, 15 Feb 2024 11:54:10 +0100 Message-ID: <875xyqq9eu.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -1.9 (-) X-Debbugs-Envelope-To: 69134-done Cc: "Afkhami, Navid" 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: -2.9 (--) Thanks for the patch. I pushed it to the master branch with commit fb79e589957880c95bb4e8e57e2a5023c8a696d6. -- Ricardo From unknown Sun Jun 22 17:11:40 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. 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