From patchwork Fri May 21 20:25:35 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29483 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 F27A827BC81; Fri, 21 May 2021 21:31:50 +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 5411127BC78 for ; Fri, 21 May 2021 21:31:50 +0100 (BST) Received: from localhost ([::1]:43754 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBoD-00020u-GB for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:31:49 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52094) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBjd-0002TY-Uh for guix-patches@gnu.org; Fri, 21 May 2021 16:27:08 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54385) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBjd-0002lK-7V 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 1lkBjb-0000DU-46 for guix-patches@gnu.org; Fri, 21 May 2021 16:27:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 03/50] gnu: r-genomicfeatures: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:27:03 +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=B48575.1621628807631 (code B ref 48575); Fri, 21 May 2021 20:27:03 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:26:47 +0000 Received: from localhost ([127.0.0.1]:37658 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjK-00009o-Dp for submit@debbugs.gnu.org; Fri, 21 May 2021 16:26:47 -0400 Received: from mail-wm1-f46.google.com ([209.85.128.46]:35337) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjG-00008R-C0 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:43 -0400 Received: by mail-wm1-f46.google.com with SMTP id z19-20020a7bc7d30000b029017521c1fb75so8082826wmk.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:42 -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=AO60ai6Yv31OKaIMJXpVdiQ7qPCI8knfx4IYHUtJGMk=; b=UPc3CAIg+9sOLID33P08jeiKPU3Vsi0B8wpPGBVxc55sH7lG3bP7kuR8vYrQA5kI2b UrmVfw6qdsC8iay2xJGU5nLDlQyF9HmVlakucIxTV/HxGU8HyraBwL153V4bIe9zuLCp QRztotUAe5OJZw5m/OOJFM9LWUIm1F0938jCXc5Ch0mPKNNituV5luer5QLSGLtTFVu3 fzuhkrArTigNwCDAlUhxsgnWaFrexR2Zb2YN8qvQB2eOCSj5LM7qFo1bmaVYbU3HVkN+ DimIvn/ZFPaHYJRi2r92O4+fYT4+NHjLcEW3LcHOiinEGnE+XXC8P53Mx1/1nVJfjBDU noZw== 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=AO60ai6Yv31OKaIMJXpVdiQ7qPCI8knfx4IYHUtJGMk=; b=R0cGoZqz/TCOokqW77+uk7AYewsMX08lshkPB2gh0s5tBklGk5iEZgVx1jorLnFgq5 jg/4kSaongQ+BUvkWgd0IvDQHn83Zn2TaNjnfiEc00u0z663EFilMZIGkNzfGefCQFgF MlXH4aGu0kQUd+fGLQwLNWd2hSye/XcCXrhjagOx7dUMievtn7BnooQS3YX/yjBL0PJ9 5IYZw4qYWzh5k+Ld91XsE6tTmbDwSsMhjhPQPRJ7wGVLLIUcIZfvEu+Vh8FKP4Jzh3Z3 u9DZqWUgpsrrMAXxh5pa8KKC0pc7KEmOh1Qk+wKRX7el9+1qqSu88DB+eAu5S79vz5Aw l2cw== X-Gm-Message-State: AOAM533oasAl5u6YkSRwqjwxhx/9liBgZ/4hNwQuEhTANacKWyYpHSQo GVeuMOx+lhmLoYmEvoEnKURoejfwvY8= X-Google-Smtp-Source: ABdhPJzmDtKKP/dUQYawI8fsWuGKFP3oI5dUST7czQg0uarTYMe0daQwMh5Nv7hyCYdV4gTaGuzQcQ== X-Received: by 2002:a05:600c:4f95:: with SMTP id n21mr10812211wmq.74.1621628796800; Fri, 21 May 2021 13:26:36 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.36 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:36 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:35 +0200 Message-Id: <20210521202622.26591-3-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-genomicfeatures): Move from here... * gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 --------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 42a3d1fffc..2263c17cc4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2108,6 +2108,49 @@ junction detection, and working with the nucleotide content of the alignments.") (license license:artistic2.0))) +(define-public r-genomicfeatures + (package + (name "r-genomicfeatures") + (version "1.42.3") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicFeatures" version)) + (sha256 + (base32 + "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz")))) + (properties + `((upstream-name . "GenomicFeatures"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GenomicFeatures") + (synopsis "Tools for working with transcript centric annotations") + (description + "This package provides a set of tools and methods for making and +manipulating transcript centric annotations. With these tools the user can +easily download the genomic locations of the transcripts, exons and cds of a +given organism, from either the UCSC Genome Browser or a BioMart +database (more sources will be supported in the future). This information is +then stored in a local database that keeps track of the relationship between +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-genomicranges (package (name "r-genomicranges") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9fb46c0d5d..bf8cb2f3a5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7849,49 +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-genomicfeatures - (package - (name "r-genomicfeatures") - (version "1.42.3") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicFeatures" version)) - (sha256 - (base32 - "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz")))) - (properties - `((upstream-name . "GenomicFeatures"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/GenomicFeatures") - (synopsis "Tools for working with transcript centric annotations") - (description - "This package provides a set of tools and methods for making and -manipulating transcript centric annotations. With these tools the user can -easily download the genomic locations of the transcripts, exons and cds of a -given organism, from either the UCSC Genome Browser or a BioMart -database (more sources will be supported in the future). This information is -then stored in a local database that keeps track of the relationship between -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-go-db (package (name "r-go-db")