From patchwork Fri May 21 20:25:58 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29467 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 DC41D27BC83; Fri, 21 May 2021 21:29:58 +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 65DB827BC78 for ; Fri, 21 May 2021 21:29:58 +0100 (BST) Received: from localhost ([::1]:39180 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBmP-0007B0-Jh for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:29:57 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52530) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkh-0004ld-JO for guix-patches@gnu.org; Fri, 21 May 2021 16:28:11 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54504) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkh-000303-C0 for guix-patches@gnu.org; Fri, 21 May 2021 16:28:11 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkh-0000Nz-95 for guix-patches@gnu.org; Fri, 21 May 2021 16:28:11 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 26/50] gnu: r-genomicfiles: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:11 +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=B48575.16216288511112 (code B ref 48575); Fri, 21 May 2021 20:28:11 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:31 +0000 Received: from localhost ([127.0.0.1]:37747 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk2-0000Hk-Rn for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:31 -0400 Received: from mail-wm1-f50.google.com ([209.85.128.50]:44795) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjQ-0000A6-HP for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:53 -0400 Received: by mail-wm1-f50.google.com with SMTP id y184-20020a1ce1c10000b02901769b409001so7810028wmg.3 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:52 -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=4/IyA5GjTj8VBRc6sNBtUWUqFF7zQtZdeCYJyfJb8Yk=; b=dJtW3S/R9waK91eigv3dmZRP1jdM/zC3E441Uh64bhh1Zpza+Wo4nGdlEqXj/tPp72 AR2K0j6P5tVFJwybzq7N/1Ab9/acd9OGntoVzfytt43Mv9FBXqR4VrQb6VJIf3g5Wa6D 4ZguuzTr/9JXJNnRXwW5f/IZ6eei+P2lLKKDgn8BrASmqtfVr4pRF1gHliuh4Dq0N2HA eghv0Hix/u4cCCHbL2rm77Ky4eX4EaO0zEs0s+qeuafAnOFRz4rqDAY29Y2gTynlOAFn xhMz1Js2gy84bodXXPOgtxfttzj5oDXpOf0KtSiB8gEOBWygcyuisP/7Fzw884wSIQSE kg9w== 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=4/IyA5GjTj8VBRc6sNBtUWUqFF7zQtZdeCYJyfJb8Yk=; b=VTLX1LXYidKXIsDobWOMKDlVfo3QHKDDcsKM34Gygv3x+5BINy+c37WnX3grcELxoL TWJAF9IaXElNRjpy5jDiec/UFzmQW7uPXngEtk9TNdiSJVAifzYHKSUm15VU0cNl7+0f nRgQWCndUfgcWjynd7F3msQqYhc/WBG3NjvBQCtYYnSPR0/7xySsky5u6mmGu7B5Qckr prWbpq4DTmzPMiVlXUPTfPbKUW7YVEHmkmPx8gKiLSiRXczEEFAGadzSL8GbaWrNxzj9 qWM9H9Q4rV0lx49JVu8YzsxfaRJ1xu7FAABQBbHhrGndI6yUToRAjZJ6NrOgXzarJhXy BHaA== X-Gm-Message-State: AOAM531n2l02yRwMqSSp8va9SyIVhgxNFM2/3zOE+oJvi+hZqbPdn8SE Ln5oa05XJTkVF3p+XTjsorAZ1Cjz1h8= X-Google-Smtp-Source: ABdhPJzhtCMAzB3kx59WtROg2BgnPbWtwU+jfiL0gd4bXRd/zRjjd5rOYG6cEsFtBcI30udyoEgDRg== X-Received: by 2002:a05:600c:4f8f:: with SMTP id n15mr2926037wmq.107.1621628807066; Fri, 21 May 2021 13:26:47 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.46 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:46 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:58 +0200 Message-Id: <20210521202622.26591-26-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-genomicfiles): Move from here... * gnu/packages/bioconductor.scm (r-genomicfiles): ...to here. --- gnu/packages/bioconductor.scm | 34 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 34 --------------------------------- 2 files changed, 34 insertions(+), 34 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 92eb5a0906..e73e78f616 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2546,6 +2546,40 @@ transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.") (license license:artistic2.0))) +(define-public r-genomicfiles + (package + (name "r-genomicfiles") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicFiles" version)) + (sha256 + (base32 + "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz")))) + (properties `((upstream-name . "GenomicFiles"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrixgenerics" ,r-matrixgenerics) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/GenomicFiles") + (synopsis "Distributed computing by file or by range") + (description + "This package provides infrastructure for parallel computations +distributed by file or by range. User defined mapper and reducer functions +provide added flexibility for data combination and manipulation.") + (license license:artistic2.0))) + (define-public r-genomicranges (package (name "r-genomicranges") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index acaf41acc4..4836eee82c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8994,40 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-genomicfiles - (package - (name "r-genomicfiles") - (version "1.26.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicFiles" version)) - (sha256 - (base32 - "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz")))) - (properties `((upstream-name . "GenomicFiles"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (home-page "https://bioconductor.org/packages/GenomicFiles") - (synopsis "Distributed computing by file or by range") - (description - "This package provides infrastructure for parallel computations -distributed by file or by range. User defined mapper and reducer functions -provide added flexibility for data combination and manipulation.") - (license license:artistic2.0))) - (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial")