From unknown Thu Jun 19 13:58:44 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#63268 <63268@debbugs.gnu.org> To: bug#63268 <63268@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add python-goatools. Reply-To: bug#63268 <63268@debbugs.gnu.org> Date: Thu, 19 Jun 2025 20:58:44 +0000 retitle 63268 [PATCH] gnu: Add python-goatools. reassign 63268 guix-patches submitter 63268 Navid Afkhami severity 63268 normal tag 63268 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Thu May 04 10:58:56 2023 Received: (at submit) by debbugs.gnu.org; 4 May 2023 14:58:56 +0000 Received: from localhost ([127.0.0.1]:51720 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1puaQ3-0003sz-Rq for submit@debbugs.gnu.org; Thu, 04 May 2023 10:58:56 -0400 Received: from lists.gnu.org ([209.51.188.17]:46694) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1puaQ0-0003so-Gr for submit@debbugs.gnu.org; Thu, 04 May 2023 10:58:54 -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 1puaPv-0002kS-D9 for guix-patches@gnu.org; Thu, 04 May 2023 10:58:50 -0400 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 1puaPs-0000Hu-AK for guix-patches@gnu.org; Thu, 04 May 2023 10:58:47 -0400 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=1683212320; x=1685026721; bh=EP05mtCdAXw6ByY bcz8JHL3p9ayjaco7gkh7BT0WHF8=; b=l86fuJ0q3MmIaGDsS9fD9MFxUNxcSfP jVosv7K/Q22ZDifJp5EodBzoxZarwjm705mb8aUbZtyuDzm015hUGBucnyTvXTk8 5ZIWv+u/honCPblUDn/MgM0U5kUQOWwOQjPu0x2y5SFUmDJhEChJJYFYoIwgioe2 RMhA5FDiNOLI= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= 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 2498A16010D for ; Thu, 4 May 2023 16:58:40 +0200 (CEST) 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 15.1.2507.23; Thu, 4 May 2023 16:58:39 +0200 From: Navid Afkhami To: Subject: [PATCH] gnu: Add python-goatools. Date: Thu, 4 May 2023 14:56:49 +0000 Message-ID: <7a9dadbaaecb1eab3d713b921a4d808154ac7f99.1683212209.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27604.006 X-TM-AS-Result: No-10--3.970400-5.000000 X-TMASE-MatchedRID: /+von0vPuFF6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt/mEPaHBc5dLwLYk+NSxc5r4qCLIu0mtIKY5ZGw7wyeHUAz MJZMjq9ZCFMmfSSkeAsign5HsLTCTuJXEeLLJ6+yrm7DrUlmNkIAy6p60ZV62fJ5/bZ6npdjKay T/BQTiGtedm1RtLCEJerUocjnTrJDnOqOQLyVYqgFpX7HAS7F81p40KFNWo7huFupi52TySp3xT 5wY6NEkBk6njH4LuHVPYzQBlrvEgt3RECuZWp8heFv61dDRnYf0c5qUjgqLKvYlQeU3xrH0XtGJ m2N/3yI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.970400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27604.006 X-TM-SNTS-SMTP: 66CC77DA035BE4741E9BDF1E1AAEDEF5E245D2EBEA8B4B660DA23B57B9C55C0B2002:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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, RCVD_IN_DNSWL_MED=-2.3, 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-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit Cc: Navid Afkhami 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: -2.4 (--) * gnu/packages/bioinformatics.scm (python-goatools): New variable. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7db8a91e80..db76d04594 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12337,6 +12337,37 @@ (define-public python-genomic-regions using the same syntax.") (license license:expat))) +(define-public python-goatools + (package + (name "python-goatools") + (version "1.3.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "goatools" version)) + (sha256 + (base32 + "1p53h7bnbmi23lcgsajf9vb8vxgjp6lmbz0hl1cx62230jvbfp62")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f)) + (propagated-inputs (list python-docopt + python-numpy + python-openpyxl + python-pandas + python-pydot + python-requests + python-scipy + python-statsmodels + python-xlsxwriter)) + (home-page "https://github.com/tanghaibao/goatools") + (synopsis "Python scripts to find enrichment of GO terms") + (description "Python scripts to find enrichment of GO terms. +In addition, this package is used for processing the +obo-formatted file from Gene Ontology website. The +data structure is a directed acyclic graph that allows +easy traversal from leaf to root.") + (license license:bsd-3))) + (define-public python-loompy (package (name "python-loompy") base-commit: f0a51a2bda26f9cc1e0b54b48712bd7cc54408e9 -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Thu May 04 13:23:49 2023 Received: (at 63268-done) by debbugs.gnu.org; 4 May 2023 17:23:49 +0000 Received: from localhost ([127.0.0.1]:51974 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pucgG-0002nY-T4 for submit@debbugs.gnu.org; Thu, 04 May 2023 13:23:49 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21016) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pucgF-0002nP-7o for 63268-done@debbugs.gnu.org; Thu, 04 May 2023 13:23:48 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1683221025; cv=none; d=zohomail.com; s=zohoarc; b=IswfL/TfkpahT5eD8dwYNn658wvjZcC+6eFEKkvoPXy8Tvmy0I7Z4Mmk2/eg8eanV1YFFo7ppmVGPyvcrNTUTOu7kmREHdtkMrLskZ3H2Eb4RCI/DVTZDsjrTHXd75ezvLrFwiVxVOYAtXGiliDNytjm/RE3KEi6Ta5BLxLJlVw= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1683221025; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=BMYNXZ+S08MBilaV/I6XzBygehG8xYv8s9HaE+5Xivc=; b=k0FsCH5op8J82jPZF57wxZriz5FsQT1+OwP4AQGUwubdhKvNX4ikku71JnkKFs4EiIc0sGqNhl0hiSzOA3MLVwP1JtYB2yzFbktkMR9YxAFL66NK77na5Hb6qRYkA1fitk/C2oX+HSX1f+/pXVEkqdwt9NgCxqFCI7CNVlCI5Sk= 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=1683221025; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=BMYNXZ+S08MBilaV/I6XzBygehG8xYv8s9HaE+5Xivc=; b=D8rOpE30UpxS5zK//UfZztwzaAN7aPsH/ZtSrW7EjZZs+K7IyUTqb3n95cUbq9Eh nVk8npg8w9jztrZNgrlDMn/b9sIGhw/B/YRT5jTdxbYycz3esjOP578/G2EddXl0kCg LJBe6KvjH+yKCRZSYg7mFA/Oq/6FtiHTV0dmCTKg= Received: from localhost (6-108-142-46.pool.kielnet.net [46.142.108.6]) by mx.zohomail.com with SMTPS id 1683221023122715.7210396863507; Thu, 4 May 2023 10:23:43 -0700 (PDT) User-agent: mu4e 1.10.2; emacs 28.2 From: Ricardo Wurmus To: 63268-done@debbugs.gnu.org Subject: [PATCH] gnu: Add python-goatools. Date: Thu, 04 May 2023 19:23:10 +0200 Message-ID: <87ttwsxb6r.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 63268-done 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: -1.0 (-) Applied with a number of changes. Thank you! -- Ricardo From unknown Thu Jun 19 13:58:44 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 02 Jun 2023 11:24:08 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator