From patchwork Fri May 21 20:26:12 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29504 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 2F8CE27BC81; Fri, 21 May 2021 21:34:04 +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 B097B27BC78 for ; Fri, 21 May 2021 21:34:03 +0100 (BST) Received: from localhost ([::1]:48422 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBqM-0005N8-UC for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:34:02 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52662) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkr-0005Tn-6B for guix-patches@gnu.org; Fri, 21 May 2021 16:28:21 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54528) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkq-00035G-T8 for guix-patches@gnu.org; Fri, 21 May 2021 16:28:20 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkq-0000Qp-OA for guix-patches@gnu.org; Fri, 21 May 2021 16:28:20 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 40/50] gnu: r-bamsignals: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:20 +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=B48575.16216288641295 (code B ref 48575); Fri, 21 May 2021 20:28:20 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:44 +0000 Received: from localhost ([127.0.0.1]:37795 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBkF-0000Kj-Vq for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:44 -0400 Received: from mail-wm1-f51.google.com ([209.85.128.51]:35356) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjX-0000Bs-Pa for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:15 -0400 Received: by mail-wm1-f51.google.com with SMTP id z19-20020a7bc7d30000b029017521c1fb75so8083132wmk.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:59 -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=sgyZSgGVQSrug9mBK3zh5vJAeo/82uG6r8r7MBgi8jM=; b=MVFF+Z0UIoJn1/js3s+UAoMuZtIzxG1o0NVGnMgJgZzNh9AXxGt5I/T1aXpLaXuPcN QTLde/lGjnh7kO6dXO3YgdjPmju/f/Kj4NQgaKLetDrB/AzqQnHpaNM6hNHo3Bsd7N+n udzaHMBwHFfm1lPY620NoUlnvIf/Y1evacSCj/nckDKehgEwvEIagN4SrRCz+V48Oxv4 hOQgxZcbqfRqOKpkOKxgVkhEXJdf7wUyTWNV4zk/5RmLtyjKrA+SGrN9DynJcqzQeJZN noopyjYgPFO0dQtOkiklcEozyXBlwvsty+WlYOnSpY6OXCstvXXNfKJPaPnCWB5uBKP3 Q0mg== 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=sgyZSgGVQSrug9mBK3zh5vJAeo/82uG6r8r7MBgi8jM=; b=Wyi9B9aIpo2nJP8q4AftHcSquZh3fVCWhE9cSukc8+LIUIG+Xlxl/3Cz/VKMQhbk+T +hFPspWw3EkpTnpT2fM0TV89GbsseiplhVQj+F/jYMPsWDDHnp1OE05V+ntW051seEix 7l+oKZvpKTy62BlnPfZ93ineTvs7hY6pZbjXPHJxLiyFObq2Kr+8hq2jSewOC3DEuwFn WvTsAeeMzakfgP+dTIOKdKvCUzVxpmNYE2hC3aPwBRQzatnFMB7iy8nNi1Eumteu3AKL Y2iT2HGltFt/l7oBSvn469LG6fCCwdAkYT+hAusbP1LGsJ4Ypr/1QjMiMsS6jpzH+oVt FaNQ== X-Gm-Message-State: AOAM531vh8Qh6n2DFLxnokCRt2t03/192RvVGp5ZK9Z5hPS+O5YnT4LB DBVOiVrfamZqhUljZNbwwX+v55o5WWs= X-Google-Smtp-Source: ABdhPJxrJCH/pNds8rqX4TRx2B0xywCdSlrvSCN/jTHY3aqrAQNjNsnTNmcQ+afeQTjRXTzf8R1YXQ== X-Received: by 2002:a05:600c:49a2:: with SMTP id h34mr10862986wmp.64.1621628813246; Fri, 21 May 2021 13:26:53 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.52 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:52 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:26:12 +0200 Message-Id: <20210521202622.26591-40-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-bamsignals): Move from here... * gnu/packages/bioconductor.scm (r-bamsignals): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e78a2a0ca..99607ba564 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1904,6 +1904,36 @@ standalone, be utilized in other packages, or be wrapped up in higher-level classes.") (license license:gpl2+))) +(define-public r-bamsignals + (package + (name "r-bamsignals") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bamsignals" version)) + (sha256 + (base32 + "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcpp" ,r-rcpp) + ("r-rhtslib" ,r-rhtslib) + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/bamsignals") + (synopsis "Extract read count signals from bam files") + (description + "This package efficiently obtains count vectors from indexed bam +files. It counts the number of nucleotide sequence reads in given genomic +ranges and it computes reads profiles and coverage profiles. It also handles +paired-end data.") + (license license:gpl2+))) + (define-public r-biobase (package (name "r-biobase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 586efcf21e..ae61ecae74 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7872,36 +7872,6 @@ including VCF header and contents in RDF and JSON.") secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-bamsignals - (package - (name "r-bamsignals") - (version "1.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "bamsignals" version)) - (sha256 - (base32 - "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/bamsignals") - (synopsis "Extract read count signals from bam files") - (description - "This package efficiently obtains count vectors from indexed bam -files. It counts the number of nucleotide sequence reads in given genomic -ranges and it computes reads profiles and coverage profiles. It also handles -paired-end data.") - (license license:gpl2+))) - (define-public r-rcas (package (name "r-rcas")