From patchwork Fri May 21 20:26:21 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29505 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 AA20827BC81; Fri, 21 May 2021 21:34:09 +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 3537227BC78 for ; Fri, 21 May 2021 21:34:09 +0100 (BST) Received: from localhost ([::1]:48768 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBqS-0005cE-Ff for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:34:08 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52650) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkq-0005Pr-Be for guix-patches@gnu.org; Fri, 21 May 2021 16:28:20 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54526) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkq-00034i-2s 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 1lkBkp-0000Qb-Vk for guix-patches@gnu.org; Fri, 21 May 2021 16:28:19 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 49/50] gnu: r-copywriter: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:19 +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=B48575.16216288631281 (code B ref 48575); Fri, 21 May 2021 20:28:19 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:43 +0000 Received: from localhost ([127.0.0.1]:37791 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBkF-0000KT-3G for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:43 -0400 Received: from mail-wm1-f54.google.com ([209.85.128.54]:50830) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjc-0000Cr-2e for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:10 -0400 Received: by mail-wm1-f54.google.com with SMTP id t206so11771448wmf.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:04 -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=4gFq4aqVkdYOI6WYtCBq/XIu0aKJKA1AIXkcYFbWkaM=; b=Z4mBLo31P+ItGlcnRTu1YHbwWC8JgDkspEQNWdmA8BEsrQTWuPZ0QrWZF+WvTR8xLF WDv09CLlnW8SxtgLmnk736KsemWFumQxoGscK2jIFemftOrApsU0uCsIU3ZUOckCsv88 uBnmN7u7Z0n9QyGN72vI5w+MeopBXMWtECh3b5y5vd7KsbPgWh8rgpfXXtLw9nm4tFV3 yDJnUDDgJOwnfcErfYS7b+Yuw5eQ5vQ4MtpEL7UBeg4fZ+KjhhEf+ZkgHNLU/EKKrl/M 93o2ZabvL/BXa5BJcv0GhTBr5I92dVdUmJhAbutaUl+YA5FLFjpZw4fV2R/kT6AMBV+M mFqA== 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=4gFq4aqVkdYOI6WYtCBq/XIu0aKJKA1AIXkcYFbWkaM=; b=q63zsbhX2lUVUaUUccDfJyDGqlsjjBkbMc2BKhvit1wsgOA08hT3JgD3ANjSoDHMJy o4/Rz8/TSL0ZFpcyjkRB84/mVMsTJhcftGmtq1iLYkoCICQB9/aRB/onkNHf/0LDqpMH caFb6W3Fz0bQvLQTGqmXYE+7uQ9syd/BCI0OReDhpFfD8ao90kX+tp1XLevpAfJma7Hv es4V1LRFrnvvjtVqscfmnnSYvVncD+F1hpmn1dTPWF1BdTuUISYvrcx8vUSiUQYXctjd wmawJMxGk9NcIk6UZG+ohJD0rLeUGwK9ayRcV7z+5eLTA+Ar/chIJUp9VIcTvydcvefK 22fw== X-Gm-Message-State: AOAM530AMf1K5num/+VxbZ6bOinsdV3hFJmxHY4+jTKR1e+Wb0MNs1kV la/LN9qb4yr3XpMOepME5QbEDZ/wFFM= X-Google-Smtp-Source: ABdhPJzdhb6PgdncYedqBGmcgb4d8wvo+1GyMYqHpVbAVy2ylHuc8Q7THY7R6xFymOrvydF+mKsTcA== X-Received: by 2002:a7b:c7ca:: with SMTP id z10mr10584604wmk.185.1621628817510; Fri, 21 May 2021 13:26:57 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.57 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:57 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:26:21 +0200 Message-Id: <20210521202622.26591-49-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-copywriter): Move from here... * gnu/packages/bioconductor.scm (r-copywriter): ...to here. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 40 --------------------------------- 2 files changed, 40 insertions(+), 40 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eee1561c1b..fe91fd486f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2295,6 +2295,46 @@ provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.") (license license:gpl2+))) +(define-public r-copywriter + (package + (name "r-copywriter") + (version "2.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CopywriteR" version)) + (sha256 + (base32 + "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f")))) + (properties `((upstream-name . "CopywriteR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-chipseq" ,r-chipseq) + ("r-copyhelper" ,r-copyhelper) + ("r-data-table" ,r-data-table) + ("r-dnacopy" ,r-dnacopy) + ("r-futile-logger" ,r-futile-logger) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/PeeperLab/CopywriteR") + (synopsis "Copy number information from targeted sequencing") + (description + "CopywriteR extracts DNA copy number information from targeted sequencing +by utilizing off-target reads. It allows for extracting uniformly distributed +copy number information, can be used without reference, and can be applied to +sequencing data obtained from various techniques including chromatin +immunoprecipitation and target enrichment on small gene panels. Thereby, +CopywriteR constitutes a widely applicable alternative to available copy +number detection tools.") + (license license:gpl2))) + (define-public r-deseq (package (name "r-deseq") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2acca0c055..79146f915f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8312,46 +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-copywriter - (package - (name "r-copywriter") - (version "2.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "CopywriteR" version)) - (sha256 - (base32 - "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f")))) - (properties `((upstream-name . "CopywriteR"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-chipseq" ,r-chipseq) - ("r-copyhelper" ,r-copyhelper) - ("r-data-table" ,r-data-table) - ("r-dnacopy" ,r-dnacopy) - ("r-futile-logger" ,r-futile-logger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://github.com/PeeperLab/CopywriteR") - (synopsis "Copy number information from targeted sequencing") - (description - "CopywriteR extracts DNA copy number information from targeted sequencing -by utilizing off-target reads. It allows for extracting uniformly distributed -copy number information, can be used without reference, and can be applied to -sequencing data obtained from various techniques including chromatin -immunoprecipitation and target enrichment on small gene panels. Thereby, -CopywriteR constitutes a widely applicable alternative to available copy -number detection tools.") - (license license:gpl2))) - (define-public r-methylkit (package (name "r-methylkit")