From patchwork Tue Apr 23 13:32:09 2024 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: 63316 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 E6BA827BBE2; Tue, 23 Apr 2024 14:34:26 +0100 (BST) 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=unavailable 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 AD9EF27BBEB for ; Tue, 23 Apr 2024 14:34:21 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rzGHm-0006k3-EF; Tue, 23 Apr 2024 09:34:14 -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 1rzGHf-0006eB-2F for guix-patches@gnu.org; Tue, 23 Apr 2024 09:34:07 -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 1rzGHe-0005Cq-2I for guix-patches@gnu.org; Tue, 23 Apr 2024 09:34:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rzGHt-0004HB-Q9; Tue, 23 Apr 2024 09:34:21 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#70536] [PATCH 2/2] gnu: Add r-seraster. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Tue, 23 Apr 2024 13:34:20 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 70536 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <70536@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 70536-submit@debbugs.gnu.org id=B70536.171387924015974 (code B ref 70536); Tue, 23 Apr 2024 13:34:20 +0000 Received: (at 70536) by debbugs.gnu.org; 23 Apr 2024 13:34:00 +0000 Received: from localhost ([127.0.0.1]:52256 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rzGHR-00047V-F8 for submit@debbugs.gnu.org; Tue, 23 Apr 2024 09:33:58 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:60579) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rzGGW-0003iM-IC for 70536@debbugs.gnu.org; Tue, 23 Apr 2024 09:33:02 -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 :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1713879153; x=1715693554; bh=/Vb5AufowFfcIUaZfNYUAiAuzZ7BJI81n58x3GHXfQI=; b=jlGRpndRczct hx9o8wz7hOv3o5kulyvC1DjWlgW+MfmDabGOBxLXjw22EdwhSZ9I+x9yHx6RKDMz hpzbafQeRK87GFqQ5khWqT2COTgya6jco4yJu6uEkRig5WBv0EqKnytaz67WdY+O 5ruSTq4G45hvhJ/2a2EPbJXsxkhMpqE= 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 C356016028D for <70536@debbugs.gnu.org>; Tue, 23 Apr 2024 15:32:33 +0200 (CEST) Received: from cl-akalin11.mdc-berlin.net (141.80.219.20) 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 15.2.1544.4; Tue, 23 Apr 2024 15:32:33 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 23 Apr 2024 15:32:09 +0200 Message-ID: <0d6e1fd7ee69b9b9751145ee2dfb039f913e0800.1713879129.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 In-Reply-To: <023204df1edfba5ec5057df74aaf43b5afca6b14.1713879129.git.madalinionel.patrascu@mdc-berlin.de> References: <023204df1edfba5ec5057df74aaf43b5afca6b14.1713879129.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.219.20] 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-14.0.0.3152-9.1.2019-28338.007 X-TM-AS-Result: No-10--8.219400-5.000000 X-TMASE-MatchedRID: n8dyCgqCzusEZ1mm50iAbnOjEKYddvv63O2+pOfl+vcwLJ9PZUBQhQMR 0wfnN/LqBfCx8jZ9Xfn6xgdq/6M9ycRHchgBhtJb6n6WKiRNqXtR3UkpERYmZG+JnhV8fY5sqV4 Bj8c7bXFQ8YI4gYfmVo0w/XXxdWgWuob7kuEJjtZGDXkz8A7djwje0Q/exjJGg322CMK8ECWaiX NQ4kfqiObIo6/v7awTyrzRjZhtElOvngkjHjojpBTT3CijgvDY28gAxP/Ts6L1VGQ8lr6yrh/88 i/oAaosQMWpQt8dMJV/PNkRUWihTiZ7wnYDVYfH8nPRrpmS7Ho= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--8.219400-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.2019-28338.007 X-TM-SNTS-SMTP: 91F9A1774AF32CA4E30348D08D9F2C9216F8135C866397722C26E4E0258B8B782000:F 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/bioconductor.scm (r-seraster): New variable. Change-Id: I345dcbdfba23b34f122d7c193604cf950fe0d8f0 --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0fca094977..828d9cfe36 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11025,6 +11025,46 @@ (define-public r-seqpattern reference point and sorted by a user defined feature.") (license license:gpl3+))) +;; This is not a Bioconductor package but it depends on three packages. +(define-public r-seraster + ;; There are no tags or releases. + (let ((commit "4fdc1ffe5d3feb65de9880329d221cf276b393a1") + (revision "1")) + (package + (name "r-seraster") + (version (git-version "0.99.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JEFworks-Lab/SEraster") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0y33lk8q0h9nfzmf7slxxvw3l0djassp4l63nsjpm3p6z4pah5s4")))) + (properties `((upstream-name . "SEraster"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-ggplot2 + r-matrix + r-rearrr + r-sf + r-spatialexperiment + r-summarizedexperiment)) + (home-page "https://github.com/JEFworks-Lab/SEraster") + (synopsis + "Rasterization framework for scalable spatial omics data analysis") + (description "SEraster is a rasterization preprocessing framework that +aggregates cellular information into spatial pixels to reduce resource requirements +for spatial omics data analysis. This package reduces the number of points in +spatial omics datasets for downstream analysis through a process of rasterization +where single cells gene expression or cell-type labels are aggregated into equally +sized pixels based on a user-defined resolution. SEraster can be incorporated +with other packages to conduct downstream analyses for spatial omics datasets, +such as detecting spatially variable genes.") + (license license:gpl3)))) + (define-public r-sesame (package (name "r-sesame")