From patchwork Thu Jan 14 19:57:44 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 26371 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 34C0C27BC12; Thu, 14 Jan 2021 19:59:27 +0000 (GMT) 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_H4,RCVD_IN_MSPIKE_WL,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 161E327BC11 for ; Thu, 14 Jan 2021 19:59:26 +0000 (GMT) Received: from localhost ([::1]:42090 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1l08mD-0006JY-2Z for patchwork@mira.cbaines.net; Thu, 14 Jan 2021 14:59:25 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:49644) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1l08lq-0006GU-HX for guix-patches@gnu.org; Thu, 14 Jan 2021 14:59:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:56059) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1l08lq-0006IO-9s for guix-patches@gnu.org; Thu, 14 Jan 2021 14:59:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1l08lq-00056R-9Y for guix-patches@gnu.org; Thu, 14 Jan 2021 14:59:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#45873] [PATCH] gnu: Add r-snapatac. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 14 Jan 2021 19:59:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 45873 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45873@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.161065430419568 (code B ref -1); Thu, 14 Jan 2021 19:59:02 +0000 Received: (at submit) by debbugs.gnu.org; 14 Jan 2021 19:58:24 +0000 Received: from localhost ([127.0.0.1]:39372 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l08lA-00055U-72 for submit@debbugs.gnu.org; Thu, 14 Jan 2021 14:58:23 -0500 Received: from lists.gnu.org ([209.51.188.17]:34740) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l08l6-00055K-6W for submit@debbugs.gnu.org; Thu, 14 Jan 2021 14:58:18 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:49450) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1l08l4-0005f6-No for guix-patches@gnu.org; Thu, 14 Jan 2021 14:58:15 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:36965) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1l08kz-000628-8o for guix-patches@gnu.org; Thu, 14 Jan 2021 14:58:14 -0500 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id 229ADA00CD; Thu, 14 Jan 2021 20:58:05 +0100 (CET) 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:received:received; s=mdc; t=1610654284; x=1612468685; bh=azIILlLbta2zED5aFbmTlfhHp6vctNkTKRsbVgfAvyU=; b=Z3ayiUQAMlUb jzMxGanv2Ds8tM0wiA7hn8ZV8Fd1oZUufNwwiA1XBXdyArN5t/VdkIDbxojN39xv whLeeXVsmIwj1n9qYG3zT5Kk8NlNXfTI2DAp5+ZRx75oGL0YvfSsiQfttNIIoZYs mYc0rajbHodUWOpR+m0K3D8KrJBJ0IY= Received: from a2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-han.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 2TUwVRnvFWAZ; Thu, 14 Jan 2021 20:58:04 +0100 (CET) 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; Thu, 14 Jan 2021 20:58:04 +0100 (CET) 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 15.1.2106.2; Thu, 14 Jan 2021 20:58:04 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Thu, 14 Jan 2021 20:57:44 +0100 Message-ID: <20210114195744.15053-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.30.0 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-14.0.0.3080-8.6.1012-25912.002 X-TM-AS-Result: No-10--0.384400-8.000000 X-TMASE-MatchedRID: 4ppMg0uMmAzRtBxlwMMWfD8Ckw9b/GFeTJDl9FKHbrmv/7fHaEp6E4qU frHU7PyNoSAZDASoRXAkrgMnNPRaLnS86kHFizFwUYXhMajr0x70IUHuSVWDh55GLlvTiXrYiMD 6wB/IizLsR+687/f48oPJHXL3hk5Z+5T6zKmlZhdcDXoTHAPnrEPIlAqA4/DEfyjNXlbBvnSgWc ErZpkOROVGjmZbJjjRj7CjdbsFOivybSXiGX6jItrZIypbofP1ojX2kLuehY2r2AvucEN0g5K1t EWloVFzDf1TH3R7beV5OPD8XJFfpL9ZdlL8eonaC24oEZ6SpSmcfuxsiY4QFF0Rqxdnqz72iLF+ KL0OzGfFDrXi9ku1Fo/kryjCBAbcgDvqJ+TsXTT2s+z39Q7BAevNMiGrMEPD9fta5byLM/Kf8ul AQx3Zb2/H7LhIKjO20bWl8H0Q2RO0ML47Km+X9EYOAQXCbpqgPpCuffGH9zI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.384400-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-25912.002 X-TM-SNTS-SMTP: E9E9D413116B0D971337DD31C86CBEB652D0ECFD72CB63362F4C9FF9632810572000: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_NONE=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: , Cc: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (r-snapatac): New variable. --- gnu/packages/bioinformatics.scm | 51 ++++++++++++++++++++++++++++++++- 1 file changed, 50 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 512abcd8fd..6be82773ac 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2017 Arun Isaac ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits -;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu +;;; Copyright © 2018, 2019, 2020, 2021 Mădălin Ionel Patrașcu ;;; Copyright © 2019, 2020 Maxim Cournoyer ;;; Copyright © 2019 Brian Leung ;;; Copyright © 2019 Brett Gilio @@ -7073,6 +7073,55 @@ sequence.") (supported-systems '("i686-linux" "x86_64-linux")) (license license:bsd-3))) +(define-public r-snapatac + (package + (name "r-snapatac") + (version "2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/r3fang/SnapATAC") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "037jzlbl436fi7lkpq7d83i2vd1crnrik3vac2x6xj75dbikb2av")))) + (properties `((upstream-name . "SnapATAC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bigmemory" ,r-bigmemory) + ("r-doparallel" ,r-doparallel) + ("r-dosnow" ,r-dosnow) + ("r-edger" ,r-edger) + ("r-foreach" ,r-foreach) + ("r-genomicranges" ,r-genomicranges) + ("r-igraph" ,r-igraph) + ("r-iranges" ,r-iranges) + ("r-irlba" ,r-irlba) + ("r-matrix" ,r-matrix) + ("r-plyr" ,r-plyr) + ("r-plot3d" ,r-plot3d) + ("r-rann" ,r-rann) + ("r-raster" ,r-raster) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rhdf5" ,r-rhdf5) + ("r-rtsne" ,r-rtsne) + ("r-scales" ,r-scales) + ("r-viridis" ,r-viridis))) + (home-page "https://github.com/r3fang/SnapATAC") + (synopsis "Single nucleus analysis package for ATAC-Seq") + (description + "This package provides a fast and accurate analysis toolkit for single +cell ATAC-seq (Assay for transposase-accessible chromatin using sequencing). +Single cell ATAC-seq can resolve the heterogeneity of a complex tissue and +reveal cell-type specific regulatory landscapes. However, the exceeding data +sparsity has posed unique challenges for the data analysis. This package +@code{r-snapatac} is an end-to-end bioinformatics pipeline for analyzing large- +scale single cell ATAC-seq data which includes quality control, normalization, +clustering analysis, differential analysis, motif inference and exploration of +single cell ATAC-seq sequencing data.") + (license license:gpl3))) + (define-public r-scde (package (name "r-scde")