From unknown Mon Jun 23 16:45:15 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#56790 <56790@debbugs.gnu.org> To: bug#56790 <56790@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add r-millefy. Reply-To: bug#56790 <56790@debbugs.gnu.org> Date: Mon, 23 Jun 2025 23:45:15 +0000 retitle 56790 [PATCH] gnu: Add r-millefy. reassign 56790 guix-patches submitter 56790 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 56790 normal tag 56790 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Wed Jul 27 04:18:14 2022 Received: (at submit) by debbugs.gnu.org; 27 Jul 2022 08:18:14 +0000 Received: from localhost ([127.0.0.1]:55054 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oGcFC-0002j5-Cc for submit@debbugs.gnu.org; Wed, 27 Jul 2022 04:18:14 -0400 Received: from lists.gnu.org ([209.51.188.17]:50390) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oGcFA-0002it-5H for submit@debbugs.gnu.org; Wed, 27 Jul 2022 04:18:13 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:54712) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oGcF9-0000ZT-VG for guix-patches@gnu.org; Wed, 27 Jul 2022 04:18:11 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:56043) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oGcF6-0000GN-0H for guix-patches@gnu.org; Wed, 27 Jul 2022 04:18:11 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1658909874; x=1660724275; bh=PCtlqTxmH2tEbT9 SDEwoWIx0qYALr/x2Z2oCp5vLDjU=; b=n4ESgTqXr3TB8u9u1G7knzAxJWM/vAf BRRwct4TuoQooTlzAaBv910TCoZzLPyHEDjo1HMi1NxMJu4ap1FmjqShPsDuJ+46 iXC2SzWlNymvqa648c5tbezTOECpDb4SoEysjJpU5Hm6sI87wqm9X9A0twVP51Xt nMLEWB7zY4GA= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 96F2DA02AC for ; Wed, 27 Jul 2022 10:17:54 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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 15.1.2507.9; Wed, 27 Jul 2022 10:17:53 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-millefy. Date: Wed, 27 Jul 2022 10:17:42 +0200 Message-ID: <20220727081742.27956-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.1 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.106] 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-14.0.0.3092-9.0.1002-27040.005 X-TM-AS-Result: No-10--4.613800-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2t6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaTSpbsSsS4oZsV8o+pqqC6J5l5tqvE/eVa87CDXaKRVJITEcvqjcF4OZYcdJgScjxJEb gebEoSmUV5MniPWJBrdWKxAF/gSPqZ67YKWwaCHH1A8E3bi1JHCbH0QLHlTYFU72YOAMDJjieAi CmPx4NwFkMvWAuahr8DV9TWrbbQmsqtq5d3cxkNRqXnrxrKCOX0AACdPVo8WUSemaHXmiRC18GL g1ITOtzPu7w01sbl7QSdvnLcIzyyhVQTea+Hd4z/PyJoAIvBRtN9sZ4s2TWOjfKeBBLjWYyDUEk BTZ8vOLxlyTCXQR4xioA5PA4dQuxuYpJR2kheXd+3BndfXUhXQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.613800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27040.005 X-TM-SNTS-SMTP: E3DDB8F97293E8448958DD597B690E312F6A6D54474CC18BEE31A2449DB52EC52002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=a2062.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 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 (r-millefy): New variable. --- gnu/packages/bioinformatics.scm | 37 ++++++++++++++++++++++++++++++++- 1 file changed, 36 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 325c159df1..cf736dfbaa 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2017, 2021, 2022 Arun Isaac ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits -;;; Copyright © 2018, 2019, 2020, 2021 Mădălin Ionel Patrașcu +;;; Copyright © 2018, 2019, 2020, 2021, 2022 Mădălin Ionel Patrașcu ;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer ;;; Copyright © 2019 Brian Leung ;;; Copyright © 2019 Brett Gilio @@ -7523,6 +7523,41 @@ (define-public r-scde ;; See https://github.com/hms-dbmi/scde/issues/38 (license license:gpl2))) +(define-public r-millefy + (package + (name "r-millefy") + (version "0.1.9-beta") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/yuifu/millefy") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0z2y0x99f761pxvg6n37cmnyrnj699jhjk43pvk05sa86iykgizl")))) + (properties `((upstream-name . "millefy"))) + (build-system r-build-system) + (propagated-inputs + (list r-data-table + r-destiny + r-dplyr + r-genomicranges + r-iranges + r-magrittr + r-rsamtools + r-rtracklayer + r-tidyr)) + (home-page "https://github.com/yuifu/millefy") + (synopsis "Make millefy plot with single-cell RNA-seq data") + (description "@code{Millefy} is a tool for visualizing read coverage of +@dfn{scRNA-seq}(single-cell RNA sequencing) datasets in genomic contexts. By +dynamically and automatically reorder single cells based on locus-specific +pseudo time, @code{Millefy} highlights cell-to-cell heterogeneity in read coverage +of scRNA-seq data.") + (license license:expat))) + (define-public r-misha (package (name "r-misha") base-commit: dbcd7876566840f31b763e28bb74394f0914b397 -- 2.37.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 01 09:24:50 2022 Received: (at 56790-done) by debbugs.gnu.org; 1 Aug 2022 13:24:50 +0000 Received: from localhost ([127.0.0.1]:39747 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oIVPe-0003OO-0y for submit@debbugs.gnu.org; Mon, 01 Aug 2022 09:24:50 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21055) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oIVPb-0003OD-96 for 56790-done@debbugs.gnu.org; Mon, 01 Aug 2022 09:24:49 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1659360284; cv=none; d=zohomail.com; s=zohoarc; b=ADfjfI+nZxwfCitzKrr9FUB0DZ4SdKqSL1xL58VRTiPNn/WwcTapXZH8HjqCHXdwHzSwi/+wR7P4WDrRuwWqjfs+vXnqwFSjHTSFEoiW+WQ77Q9N5xg3d0VsuPJJ9vYPJ9BFq9gQs+xY8RwEvnLv41+k16LrfgfnDcPC+HZz7Z8= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1659360284; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=T26Mi1Dv4dJ8yP7d8wi1DfNRdxQAn1fLjGLO++tnC5k=; b=bXiwhAtspSQmwAfADegfXbF1ooHSuYln/w1qF/DTZ0UUjYOfoyqh9ohKaogggvSuk+bjo+rj6RZ0YoaYYng2RlKh81e/FiUn62M8qPRpIKCEzgLi3wYXs8LBI57EKwqWgA3nfhXAdBWg7X1J25gny6jVVP5e2AJbNCr3sSE/31g= 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=1659360284; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To; bh=T26Mi1Dv4dJ8yP7d8wi1DfNRdxQAn1fLjGLO++tnC5k=; b=YBDfqrqBdLMrWD4Rt0tjIXugnByoWtr82hGkgivByl+U6rFSN9xgCxCfTVGCRD7W pjRV7QIns+TLoaYSc9H6j43uF+leZlvf669qrxjKmHGGVYWTg7Ufp1BJdOsRcVR9wtW ibIUcwvYsX0/FEu6V5s7L7WXQH1uNhILgUWQoG9Y= Received: from localhost (i5E862C69.versanet.de [94.134.44.105]) by mx.zohomail.com with SMTPS id 1659360281797915.5241895747282; Mon, 1 Aug 2022 06:24:41 -0700 (PDT) References: <20220727081742.27956-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.6.11; emacs 28.1 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#56790] [PATCH] gnu: Add r-millefy. Date: Mon, 01 Aug 2022 15:24:03 +0200 In-reply-to: <20220727081742.27956-1-madalinionel.patrascu@mdc-berlin.de> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87sfmgnlk9.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 56790-done Cc: 56790-done@debbugs.gnu.org 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 (-) > * gnu/packages/bioinformatics.scm (r-millefy): New variable. Applied, thanks! -- Ricardo From unknown Mon Jun 23 16:45:15 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Tue, 30 Aug 2022 11:24:11 +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