From patchwork Fri May 21 20:25:33 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29456 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 E789027BC81; Fri, 21 May 2021 21:27:54 +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 6558627BC78 for ; Fri, 21 May 2021 21:27:54 +0100 (BST) Received: from localhost ([::1]:34424 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBkP-0003e9-I6 for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:27:53 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52096) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBjd-0002Ta-V7 for guix-patches@gnu.org; Fri, 21 May 2021 16:27:08 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54383) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBjc-0002lJ-RE for guix-patches@gnu.org; Fri, 21 May 2021 16:27:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBja-0000DN-NY for guix-patches@gnu.org; Fri, 21 May 2021 16:27:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 01/50] gnu: r-genomicalignments: Move to (gnu packages bioconductor). References: <20210521202136.26524-1-zimon.toutoune@gmail.com> In-Reply-To: <20210521202136.26524-1-zimon.toutoune@gmail.com> Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:27:02 +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=B48575.1621628806612 (code B ref 48575); Fri, 21 May 2021 20:27:02 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:26:46 +0000 Received: from localhost ([127.0.0.1]:37653 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjJ-00009I-27 for submit@debbugs.gnu.org; Fri, 21 May 2021 16:26:46 -0400 Received: from mail-wm1-f53.google.com ([209.85.128.53]:39496) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjF-00008P-V3 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:43 -0400 Received: by mail-wm1-f53.google.com with SMTP id l18-20020a1ced120000b029014c1adff1edso8057867wmh.4 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:41 -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:mime-version :content-transfer-encoding; bh=96ryHvppI/z/svia7102m8CmVmrjcXgYuzJiXt9wTTc=; b=Nl+MzmJ2HXHezlDYlzkiXu2QwEFEFpMwrGPaKgJU+grDPwNpb+ugXFrODFUWo8gfHY ikScLu+2hjFBICvP6rp9EJ+fnjV9aBWcqQPRmmdiM0Y4Z9ezOQV6pYmAS9M2NHfR3gyH mtq9NMZTVjsFw+GP1OTLQ0FbCho6XUgBYMK/ZBIaiwA4ga8uwmkbSgEfzcwex+EVwXFy E9Badx0Zh2LgX2VOkz/r00e0nVqmQWc9pB3wRy+kL3/fCnBhyo74bt+6DD03T1pbdVbv AC8HMAA6ZP/QBafum0ZpecJux/X5oVqQmPWs+2zsWedVsjxj77+NWczCE4YPUZi2WSWG riXw== 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:mime-version :content-transfer-encoding; bh=96ryHvppI/z/svia7102m8CmVmrjcXgYuzJiXt9wTTc=; b=FljrsCVRf9PDFa1bKhReCQQyq6DkT45fU87JeNkEuapay3CQVyp/TldrJf7mZXSYFK lLTJDwZj1aBscbwttrypeSfl6VFzPi4RKRMYqkEa7g0/r76c8lNsMN9TKJo2GgOaORTC sDJWDTg5ohxtK22bwdeX4h0VVJBiCFHjjmEeAUrrfWGYAe6bePj9vyKjuQVGKuFLilAL dFkpH/74JXKubZT1Gz2UpVGInGABg9sQORSTfoLJIpklwSmM4ZwC6w07wSS67a42x+ds +4DrSLpQhO1d631UvkAS7EHQFyy9kSDXyw8pFfsZa/NI2LDS2WTZ7z/Py+0pimHEWs5D yMFQ== X-Gm-Message-State: AOAM530ufECfkkkdxgB+fRPcmry87JcFaRvEhZvKOiuR3DRgImDYi7A6 K1qjagCJNnL5+KQc40fsC3rvmgQJR7I= X-Google-Smtp-Source: ABdhPJxq1bow5xEdfUhZrd3iLR8WXZobKyfJllzY3DgHYEc6eYrC19buphz6h504w518uIuXuXuk8w== X-Received: by 2002:a7b:c7ca:: with SMTP id z10mr10583698wmk.185.1621628795867; Fri, 21 May 2021 13:26:35 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.35 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:35 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:33 +0200 Message-Id: <20210521202622.26591-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 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-genomicalignments): Move from here... * gnu/packages/bioconductor.scm (r-genomicalignments): ...to here. --- gnu/packages/bioconductor.scm | 35 ++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 33 ------------------------------- 2 files changed, 34 insertions(+), 34 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 45e31a5760..4f4ff82ad0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft @@ -2075,6 +2075,39 @@ translation between different chromosome sequence naming conventions (e.g., names in their natural, rather than lexicographic, order.") (license license:artistic2.0))) +(define-public r-genomicalignments + (package + (name "r-genomicalignments") + (version "1.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicAlignments" version)) + (sha256 + (base32 + "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr")))) + (properties + `((upstream-name . "GenomicAlignments"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/GenomicAlignments") + (synopsis "Representation and manipulation of short genomic alignments") + (description + "This package provides efficient containers for storing and manipulating +short genomic alignments (typically obtained by aligning short reads to a +reference genome). This includes read counting, computing the coverage, +junction detection, and working with the nucleotide content of the +alignments.") + (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 9c77d66a35..0d0fe1df30 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7849,39 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomicalignments - (package - (name "r-genomicalignments") - (version "1.26.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicAlignments" version)) - (sha256 - (base32 - "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr")))) - (properties - `((upstream-name . "GenomicAlignments"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (home-page "https://bioconductor.org/packages/GenomicAlignments") - (synopsis "Representation and manipulation of short genomic alignments") - (description - "This package provides efficient containers for storing and manipulating -short genomic alignments (typically obtained by aligning short reads to a -reference genome). This includes read counting, computing the coverage, -junction detection, and working with the nucleotide content of the -alignments.") - (license license:artistic2.0))) - (define-public r-rtracklayer (package (name "r-rtracklayer")