From patchwork Fri May 21 20:26:19 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29481 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 0468C27BC83; Fri, 21 May 2021 21:31:26 +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 8C18027BC78 for ; Fri, 21 May 2021 21:31:25 +0100 (BST) Received: from localhost ([::1]:43280 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBno-0001ha-Ou for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:31:24 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52640) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkp-0005Kn-7F for guix-patches@gnu.org; Fri, 21 May 2021 16:28:19 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54523) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBko-00034A-TG for guix-patches@gnu.org; Fri, 21 May 2021 16:28:18 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBko-0000QF-Q3 for guix-patches@gnu.org; Fri, 21 May 2021 16:28:18 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 47/50] gnu: r-chipseq: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:18 +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=B48575.16216288621257 (code B ref 48575); Fri, 21 May 2021 20:28:18 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:42 +0000 Received: from localhost ([127.0.0.1]:37785 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBkA-0000K4-Mz for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:42 -0400 Received: from mail-wm1-f48.google.com ([209.85.128.48]:43644) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjb-0000Cd-1F for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:09 -0400 Received: by mail-wm1-f48.google.com with SMTP id z85-20020a1c7e580000b029017a76f3afbaso5255032wmc.2 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:02 -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=iaH+3sal2krXTGH2XpmYQLHIK0r2pEqsyUwvzT1KVyo=; b=iZdRj8zAUI7o6OwWdrmX3aOPdKIaTLIqMlaY4R9iRG5A9qtdfIjtKGSU7cb88HLVXR jbksJeKQi9lFiHQ2XjT7IJoTFeEhrLOPu9w/jm6rfXxM5hLHsR7CDRprtBDc0U1HhcR4 uBEtHOEpKGXF75QU4riPGM7O1OY5ugjc/oxxEXQeNcBNI0zW+rXPa3N4yO/xwuNYDDrK YswAaldqf9WiIntssft904Wfrv1UFzfWD07IqgW8Gh5m2xQ/yVE3vtWLlwP066Z8WVjm 0Eyj7XquQC6AMWdxqJykYlPHSP9IOEreogDiSZvpnTweVQl7GAChrEgPB6eJnD5OSJh9 G7jg== 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=iaH+3sal2krXTGH2XpmYQLHIK0r2pEqsyUwvzT1KVyo=; b=V9/bHkfUOQ+Q1hutzpcHY2bRYLi4RQXMMmN0d0wxktEUtiLnj7hauqnmb8VEkjyT8E cHweVr3OTYqI+zh0oOc7ZjXMi9B2Hwp6Kl4DcImm58uZXpHeyQZmctLm0XxyQg/7iDpl /ZT+xoKTxwebA2WrKRTMsEe/rFdda752I8/lqzyKSHfuWtBjYDatTWgr9z+TxhwpB9LI kahqdEsVs7VIC3t2h2ntzmFarcyVitiwn8q1LjWJsIKpEGVXPKJOQdxnd5bcWzQgkFnZ piZn7K25qN13xMD7RKoybDFsbinj9Sa/ZGJ/XxctbfM8xpgkLgL/zoVQe0MiuUq2VCm9 P39w== X-Gm-Message-State: AOAM530DzkHJ8/pH0hKNlLhqUhx+inLhBCaUFl/zZcCCVvvcAz0hwVt3 VVkYMuVKH6Q+Hhi2tBKys1WUPwCRAkE= X-Google-Smtp-Source: ABdhPJxAFYv+YKQKHeJkYUtV0Q2/YuuUbCMOunXN59pFUJOnbb5HPVQ7HXMxSsoNCUXzFd6YCwIjPQ== X-Received: by 2002:a1c:e912:: with SMTP id q18mr10856343wmc.59.1621628816514; Fri, 21 May 2021 13:26:56 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.56 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:56 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:26:19 +0200 Message-Id: <20210521202622.26591-47-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-chipseq): Move from here... * gnu/packages/bioconductor.scm (r-chipseq): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d027a24bf3..f224a5ecb4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2206,6 +2206,32 @@ genome data packages and support for efficient SNP representation.") analysis.") (license license:artistic2.0))) +(define-public r-chipseq + (package + (name "r-chipseq") + (version "1.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "chipseq" version)) + (sha256 + (base32 + "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-s4vectors" ,r-s4vectors) + ("r-shortread" ,r-shortread))) + (home-page "https://bioconductor.org/packages/chipseq") + (synopsis "Package for analyzing ChIPseq data") + (description + "This package provides tools for processing short read data from ChIPseq +experiments.") + (license license:artistic2.0))) + (define-public r-complexheatmap (package (name "r-complexheatmap") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ef0d7b3007..3ee3d9d4f3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8312,32 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-chipseq - (package - (name "r-chipseq") - (version "1.40.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "chipseq" version)) - (sha256 - (base32 - "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread))) - (home-page "https://bioconductor.org/packages/chipseq") - (synopsis "Package for analyzing ChIPseq data") - (description - "This package provides tools for processing short read data from ChIPseq -experiments.") - (license license:artistic2.0))) - (define-public r-copyhelper (package (name "r-copyhelper")