From patchwork Fri May 21 20:25:37 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29457 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 92B0127BC78; Fri, 21 May 2021 21:28:13 +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 0E03027BC83 for ; Fri, 21 May 2021 21:28:13 +0100 (BST) Received: from localhost ([::1]:35490 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBki-0004Mb-7c for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:28:12 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52418) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkZ-0004IC-8V for guix-patches@gnu.org; Fri, 21 May 2021 16:28:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54483) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkZ-0002vm-15 for guix-patches@gnu.org; Fri, 21 May 2021 16:28:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkY-0000LT-TL for guix-patches@gnu.org; Fri, 21 May 2021 16:28:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 05/50] gnu: r-bsgenome: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:02 +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=B48575.1621628831930 (code B ref 48575); Fri, 21 May 2021 20:28:02 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:11 +0000 Received: from localhost ([127.0.0.1]:37704 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjh-0000EV-LL for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:10 -0400 Received: from mail-wm1-f48.google.com ([209.85.128.48]:36534) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjH-00008U-7q for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:45 -0400 Received: by mail-wm1-f48.google.com with SMTP id n17-20020a7bc5d10000b0290169edfadac9so8084325wmk.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:43 -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=4gsQxzbRuhpoQd5rSV88rS+SfboPlsJKOXw3pQsN0rg=; b=EA/3rapxM0eaeGr0xK1X1Lm+kuaUsaRetC0sU1KGP8wP9HCANdrwcbUO9scBSAXwlG n+Aw280FYrpg5snqtjD2gMlFlS3qrzSbvlUCmo88LDsviBTWSGYC/VY2KxnZIL7MUpGA SIi7c/qKcS3FkrKf0oNZRV3SOZieDg2xkzr8/lzKYYS800qtXfSPZWlM5g9yG7wbFeyS 2jAwZjjKcjN4S2rKWY2bj8YOdF4jtOZS2ajcFb2TrDxRfp5Gj7u7kt3NjWuSC90QFguR c6+f0Ghn8n5mGa2C7iLYjVhwO2CZOZ93dSr2TPQPgllHlm1/hLd3w3tVKYh4fpR4jrSv ettw== 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=4gsQxzbRuhpoQd5rSV88rS+SfboPlsJKOXw3pQsN0rg=; b=Wii9J3XwzQky8ieIuqSyCvyZhXnyBGJru+apGt7EDB8IPXhoF8Q491cs/65D4t709z +ydWpK+oltgL+yB0VIDFMr9YN1dhI9P6ehiAD7hr1kshUOECi7t7IC6pEjFEopM6ACaL hb1lm38hutxS+It9Q+QneTxIDy/2Y5eoIRDV1tszS48XE6qaHLIZu4UNElv2fUn03ufm jSLAxV5gxWjdI+v6J2uoW+LZAsY11rEMxHJ/F3CcJqfSRDV+ZbKXcVpzt07Uwb9Dp7Ey orDZ5g/HgEwRYM22TRNaLbJPwPhLAIO/dcycE8xva1n2UIBYYloByhrSpd6aH0pt3Hps uF2w== X-Gm-Message-State: AOAM531kpeL1DNlPfM2ZU++3qkEBvAGqsKsnkcWgre/dqHLghjdI6CV4 K1dVdYItty8KoxBX6NSPTiAQD1fKvUA= X-Google-Smtp-Source: ABdhPJyEWP8ZutIDQIZ3A+Nf38Dai+D6Z0pOqZxODonLwt4aU6kVeY7haMlBgtvXSLMRi+UHrCfkZA== X-Received: by 2002:a7b:c3d4:: with SMTP id t20mr9931688wmj.13.1621628797701; Fri, 21 May 2021 13:26:37 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.37 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:37 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:37 +0200 Message-Id: <20210521202622.26591-5-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-bsgenome): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome): ...to here. --- gnu/packages/bioconductor.scm | 33 ++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2afb5214ee..923413135b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017 Efraim Flashner -;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu @@ -1875,6 +1875,37 @@ matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.") (license license:artistic2.0))) +(define-public r-bsgenome + (package + (name "r-bsgenome") + (version "1.58.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome" version)) + (sha256 + (base32 + "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq")))) + (properties + `((upstream-name . "BSgenome"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/BSgenome") + (synopsis "Infrastructure for Biostrings-based genome data packages") + (description + "This package provides infrastructure shared by all Biostrings-based +genome data packages and support for efficient SNP representation.") + (license license:artistic2.0))) + (define-public r-category (package (name "r-category") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 32d2b6a683..9c9288c6b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7873,37 +7873,6 @@ including VCF header and contents in RDF and JSON.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-bsgenome - (package - (name "r-bsgenome") - (version "1.58.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BSgenome" version)) - (sha256 - (base32 - "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq")))) - (properties - `((upstream-name . "BSgenome"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/BSgenome") - (synopsis "Infrastructure for Biostrings-based genome data packages") - (description - "This package provides infrastructure shared by all Biostrings-based -genome data packages and support for efficient SNP representation.") - (license license:artistic2.0))) - (define-public r-impute (package (name "r-impute")