From patchwork Thu Oct 28 15:12:04 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 34125 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 C105E27BBE3; Thu, 28 Oct 2021 16:16:49 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS,T_DKIM_INVALID, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 54D6327BBE1 for ; Thu, 28 Oct 2021 16:16:49 +0100 (BST) Received: from localhost ([::1]:48846 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1mg796-0004fu-9v for patchwork@mira.cbaines.net; Thu, 28 Oct 2021 11:16:48 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40796) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mg75T-0000hO-HU for guix-patches@gnu.org; Thu, 28 Oct 2021 11:13:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:41381) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1mg75T-0000NB-87 for guix-patches@gnu.org; Thu, 28 Oct 2021 11:13:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1mg75S-0003p7-3q for guix-patches@gnu.org; Thu, 28 Oct 2021 11:13:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#51461] [PATCH] gnu: Add r-zellkonverter. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 28 Oct 2021 15:13:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 51461 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 51461@debbugs.gnu.org Cc: rekado@elephly.net, =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmE=?= =?utf-8?b?yJljdQ==?= X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.163543398014687 (code B ref -1); Thu, 28 Oct 2021 15:13:01 +0000 Received: (at submit) by debbugs.gnu.org; 28 Oct 2021 15:13:00 +0000 Received: from localhost ([127.0.0.1]:52926 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mg75Q-0003op-3G for submit@debbugs.gnu.org; Thu, 28 Oct 2021 11:13:00 -0400 Received: from lists.gnu.org ([209.51.188.17]:45894) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mg75L-0003of-RT for submit@debbugs.gnu.org; Thu, 28 Oct 2021 11:12:57 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40754) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mg75L-0000GT-F2 for guix-patches@gnu.org; Thu, 28 Oct 2021 11:12:55 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:54581) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mg757-0000KO-7m for guix-patches@gnu.org; Thu, 28 Oct 2021 11:12:54 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 9D23B300106; Thu, 28 Oct 2021 17:12:23 +0200 (CEST) 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:received:received; s=mdc; t=1635433943; x=1637248344; bh=GrtpmfBgOVQ0ItIn9MEXNXQdY4y71DtaW7anwPptB6E=; b=kXKq8urDFfwi aXfJVZykj+R6wiI1lZYm6IazUrtgJqZkmhL9NiUGx/ge8tZoxl2ZOayIRMT2xZGI PQh8BBsu/BjaBsWADxCl6uDKVQzIFmkNFIbU1IvlYDBNUZFJL8epNZ26Hab+p8v5 mvDlHbzE2OeZC9z2jKHk/Nj0CqmgKX4= Received: from c2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-erl.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id uau1eHdGKWEo; Thu, 28 Oct 2021 17:12:23 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS; Thu, 28 Oct 2021 17:12:23 +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 15.1.2308.15; Thu, 28 Oct 2021 17:12:22 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Thu, 28 Oct 2021 17:12:04 +0200 Message-ID: <20211028151204.23167-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.33.0 MIME-Version: 1.0 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-14.0.0.3092-8.6.1018-26496.000 X-TM-AS-Result: No-10--2.724900-8.000000 X-TMASE-MatchedRID: xPvPRJicGCQsaaYlMvaOHAPZZctd3P4Bzv7O27to65Hhbc38imJFQWim Izb1qb1PRRa406V/YwwKl5/g/W44hrJJ3aMCJ9Hhz5r5y9mouSAqSb58EIanQJf69fQNowiyiMD 6wB/IizJ05yZ49kHVQYn0O0NmxwZcoGg41PayguRqZ6OipRp3egnYwtywxoaBXum7C/z4OuoKVW Bv5DfSi0nJmQjzpbL45U1Na/wV3XrQ3sOMB3Fk1OLzNWBegCW2wgn7iDBesS3CttcwYNipXw2y0 JeZ/zsccDYDfzGdpRWAc6iA1BeMEEhxrW1lc0K0/XwC2pQeCWsBUyzmmPIVQPas6TFIUX33QO2F mK1q1B+bKH8vxmdSaZa9FqNDarg0xsbRsxJFgNYWGegpbh/sx/VzxEkh5LVAWYqZ+nM0cw0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.724900-8.000000 X-TMASE-Version: SMEX-14.0.0.3092-8.6.1018-26496.000 X-TM-SNTS-SMTP: 65E19B150EDCD2459031B2D0B0D3FF3F23F6DAD0F6160EA577B8C72E048CC3BC2000:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=c2062.mx.srv.dfn.de X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 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, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action 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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-zellkonverter): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 90a0e1f288..ce3a4badce 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4682,6 +4682,38 @@ (define-public r-zlibbioc libraries for systems that do not have these available via other means.") (license license:artistic2.0))) +(define-public r-zellkonverter + (package + (name "r-zellkonverter") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "zellkonverter" version)) + (sha256 + (base32 "1ihp2f23lpdfgf3qliy22vrq8czm353hyhqf74r5r712190k6pgg")))) + (properties `((upstream-name . "zellkonverter"))) + (build-system r-build-system) + (propagated-inputs + `(("r-basilisk" ,r-basilisk) + ("r-cli" ,r-cli) + ("r-delayedarray" ,r-delayedarray) + ("r-matrix" ,r-matrix) + ("r-reticulate" ,r-reticulate) + ("r-s4vectors" ,r-s4vectors) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/theislab/zellkonverter") + (synopsis "Conversion between AnnData and single-cell experiments objects") + (description + "This package provides methods to convert between Python AnnData objects +and SingleCellExperiment objects. These are primarily intended for use by +downstream Bioconductor packages that wrap Python methods for single-cell data +analysis. It also includes functions to read and write H5AD files used for +saving AnnData objects to disk.") + (license license:expat))) + (define-public r-geneplotter (package (name "r-geneplotter")