From patchwork Fri May 21 20:25:42 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29460 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 D843227BC81; Fri, 21 May 2021 21:28:22 +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_ADSP_CUSTOM_MED, DKIM_SIGNED,FREEMAIL_FROM,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 36F6A27BC78 for ; Fri, 21 May 2021 21:28:22 +0100 (BST) Received: from localhost ([::1]:36274 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBkr-000519-AT for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:28:21 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52428) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBka-0004M4-Tg for guix-patches@gnu.org; Fri, 21 May 2021 16:28:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54487) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBka-0002wJ-MJ for guix-patches@gnu.org; Fri, 21 May 2021 16:28:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBka-0000Lx-Ij for guix-patches@gnu.org; Fri, 21 May 2021 16:28:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 10/50] gnu: r-seqpattern: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48575 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 48575@debbugs.gnu.org Cc: zimoun Received: via spool by 48575-submit@debbugs.gnu.org id=B48575.1621628832960 (code B ref 48575); Fri, 21 May 2021 20:28:04 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:12 +0000 Received: from localhost ([127.0.0.1]:37712 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjk-0000FJ-5P for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:12 -0400 Received: from mail-wm1-f47.google.com ([209.85.128.47]:43629) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjJ-00008b-F1 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:46 -0400 Received: by mail-wm1-f47.google.com with SMTP id z85-20020a1c7e580000b029017a76f3afbaso5254727wmc.2 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:45 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=oJpu37ZGZSHienBIpUNS1smzwtnN+P+v9Fbp2Aa9ihw=; b=u63C2jazNgnlGPEyrLGVj6nVi3ArY8nRKv3YAz1k3h2XXXHefde4mljiaTJM3Yxeu1 /uhFmTF3Y5o86U7qm3G+VFuWE0Kjg2YYQObpDAtu+w+SJpDg8nxDx0DmIS8QquUqoLs9 Mg4fwjh/GNFkFgzYoH7zeSQcA3SURU91McNdCSIux3vifRJgGzLDswsiEwF5gd4/geBE 4zye9g6L//RpqJdGQjDXMTjacr8aqrfzf5Tw5tXdIlmkDT2T+HXdI4D+OhyITtjHvh3A s1xc9M440ESXQHfSyy9Q2F0ry7xAkM6+lTCDMO7CnJyJVEC9twx+rWv18tnTYnXDyqhA LPzA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=oJpu37ZGZSHienBIpUNS1smzwtnN+P+v9Fbp2Aa9ihw=; b=CU5K+eiwhz7Le5SlQrbhANAcfzRbVnVpHU3oZAt9AIbIoLVTlJB/lcrTeYt4zh6dzx yvKsIwPUhwizXBjAExKUpajC/ZZrdZK0/tUTv16n8U6inrT8LeVT6kJ2tGcKqYKhaanr dhmJJrF//ASnMUAX7D8NnGyJ6YEO8DMIBKuzrGGL3GKOWDLybPBGgdHm3pAqb8nIvxo+ 9KFYlk1b3PHrHlWY/sXQ8IrJniqXt35Aa5n9WJrb2D/WxnjTB4JOW/XDymrSjU71GaqO RIawBQkvnQh13PHjw2h5P+NniwjmNSKUzmi6HjLmqKEUtfeLu5QhJYwBLWD9g1KSo3f5 Btaw== X-Gm-Message-State: AOAM5329SThS4zQfSBR4YdcFtf+VKtJRtygY1V45pUMUrShbwdYcBvby BbOs7lyLXheci5JsGPvllu8Yjv3FyLg= X-Google-Smtp-Source: ABdhPJz+Srv90X+ctq/pQBNlTUlADCRkgOVXH5ygTkYp/PtL+rOUk2WTQYN2mSDBETHQOMQW2Kg9qA== X-Received: by 2002:a05:600c:3227:: with SMTP id r39mr10335501wmp.26.1621628799950; Fri, 21 May 2021 13:26:39 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.39 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:39 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:42 +0200 Message-Id: <20210521202622.26591-10-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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/bioinformatics.scm (r-seqpattern): Move from here... * gnu/packages/bioconductor.scm (r-seqpattern): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0b40d70397..1b1b00cde0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2655,6 +2655,33 @@ differential expression analysis, RNAseq data and related problems.") ;; Any version of the LGPL (license license:lgpl3+))) +(define-public r-seqpattern + (package + (name "r-seqpattern") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "seqPattern" version)) + (sha256 + (base32 + "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq")))) + (properties + `((upstream-name . "seqPattern"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-kernsmooth" ,r-kernsmooth) + ("r-plotrix" ,r-plotrix))) + (home-page "https://bioconductor.org/packages/seqPattern") + (synopsis "Visualising oligonucleotide patterns and motif occurrences") + (description + "This package provides tools to visualize oligonucleotide patterns and +sequence motif occurrences across a large set of sequences centred at a common +reference point and sorted by a user defined feature.") + (license license:gpl3+))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ef5c1a3323..71e1481af2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7873,33 +7873,6 @@ including VCF header and contents in RDF and JSON.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-seqpattern - (package - (name "r-seqpattern") - (version "1.22.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "seqPattern" version)) - (sha256 - (base32 - "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq")))) - (properties - `((upstream-name . "seqPattern"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-plotrix" ,r-plotrix))) - (home-page "https://bioconductor.org/packages/seqPattern") - (synopsis "Visualising oligonucleotide patterns and motif occurrences") - (description - "This package provides tools to visualize oligonucleotide patterns and -sequence motif occurrences across a large set of sequences centred at a common -reference point and sorted by a user defined feature.") - (license license:gpl3+))) - (define-public r-genomation (package (name "r-genomation")