From patchwork Mon Mar 15 13:01:58 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27705 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 C86C627BC52; Mon, 15 Mar 2021 13:03:33 +0000 (GMT) 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_H3, 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 5A17D27BC55 for ; Mon, 15 Mar 2021 13:03:28 +0000 (GMT) Received: from localhost ([::1]:38608 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLmsZ-000333-It for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 09:03:27 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:60050) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLmsD-00032V-LC for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51750) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLmsC-0007I2-J8 for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLmsC-0006Cj-Gb for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47156] [PATCH 10/10] gnu: r-variantannotation: Move to (gnu packages bioconductor). References: <20210315125800.30246-1-zimon.toutoune@gmail.com> In-Reply-To: <20210315125800.30246-1-zimon.toutoune@gmail.com> Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 13:03:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47156 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47156@debbugs.gnu.org Cc: zimoun Received: via spool by 47156-submit@debbugs.gnu.org id=B47156.161581333723750 (code B ref 47156); Mon, 15 Mar 2021 13:03:04 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:02:17 +0000 Received: from localhost ([127.0.0.1]:35058 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrQ-0006B0-KQ for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:17 -0400 Received: from mail-wm1-f47.google.com ([209.85.128.47]:34392) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrL-0006AJ-VG for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:12 -0400 Received: by mail-wm1-f47.google.com with SMTP id n11-20020a05600c4f8bb029010e5cf86347so2262755wmq.1 for <47156@debbugs.gnu.org>; Mon, 15 Mar 2021 06:02:11 -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=UktbsVBAxsuPXyhqSuueZQiphjwVwYsVljVSaG2Z2Tc=; b=edF4R77ZkiHa4vfNDeHXJZqowUqd0svzEy4067TgH1fiytTWH6H9bDEyFXL55rCmAq Uuyd0PUx49ZQ9sJD7dgj0PL9Cgv+umX8vFnyKMq8+AieKO+P1wWpVsmMOXj6dwJVkm3H 2Gz5God75zfkpMlfmNg00S6lfLPelhJcWikUnFp/Yrhp2CcGXfQVxDVaSvh0cKpYoU92 91Cb/p5NPrDAN4PCA53CLSNeujnT1+OnElzAqdzJhqmgx7ySbpnhVBrWDWhSBMWKJQ34 4xIXy8msNmGHZTwPILc0iUXmrFfabB9Kh7OqzKHxFQSKjl4fY9gUzXRS8tBegsnjA1Rj 0zsw== 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=UktbsVBAxsuPXyhqSuueZQiphjwVwYsVljVSaG2Z2Tc=; b=XAa3RiYqXwb9B2UNA0bk3pf7jvfuN/mIIvBatDdF+xdzowbjGy5k5LMzp1nI0NWuUJ wfIGD77Y/eFt4Elvpg33zXUhD58i2ADU7az93QkC7hFdRfOPcms9+oJRoirg5uAcs6gx CGzTRAHSsNJjJVKSZfFcRnoFYlwcefLgRgxzbhu/q7FGiDqVXFCpSAnrTp8tebRRLQji O/KSRClrfJpczHf787NjjO0sNYynPOGgEhfs7tCQDptDYuhqjXGU9EJ8D8SbWtUuviOG RnfLEU77cMW3MkI2TMn/QmiYNmCyGk++A0nNEyLuhGnLNhZHUv1xiWx0gtVeND/CBrAm VIaQ== X-Gm-Message-State: AOAM533/VoHD22R51GGCNk3KLG2VABIWHKPjW9BOGgJFtAN4b4RuBAk0 PIg4HqMfoZY0pOI6QYHsloqbQtr58og= X-Google-Smtp-Source: ABdhPJx4oxitsYHCy5LmVF4hSrJMTe1vNieEiWvuL6hXBGMnmyfCzcytaiDJH1unenLyyG4XUoM+wA== X-Received: by 2002:a1c:3d46:: with SMTP id k67mr20794739wma.188.1615813320909; Mon, 15 Mar 2021 06:02:00 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id c9sm18682463wrr.78.2021.03.15.06.02.00 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 06:02:00 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 14:01:58 +0100 Message-Id: <20210315130158.30365-1-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-variantannotation): Move from here... * gnu/packages/bioconductor.scm (r-variantannotation): ...to here. --- gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 38 --------------------------------- 2 files changed, 38 insertions(+), 38 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fb0127b7ca..c4df090a05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2051,6 +2051,44 @@ experimental designs is facilitated by a consistently implemented sample annotation infrastructure.") (license license:artistic2.0))) +(define-public r-variantannotation + (package + (name "r-variantannotation") + (version "1.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "VariantAnnotation" version)) + (sha256 + (base32 + "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw")))) + (properties + `((upstream-name . "VariantAnnotation"))) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrixgenerics" ,r-matrixgenerics) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-rhtslib" ,r-rhtslib) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector) + ("r-zlibbioc" ,r-zlibbioc))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/VariantAnnotation") + (synopsis "Package for annotation of genetic variants") + (description "This R package can annotate variants, compute amino acid +coding changes and predict coding outcomes.") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dc0d7a2906..78df3091fe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,44 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-variantannotation - (package - (name "r-variantannotation") - (version "1.36.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "VariantAnnotation" version)) - (sha256 - (base32 - "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw")))) - (properties - `((upstream-name . "VariantAnnotation"))) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/VariantAnnotation") - (synopsis "Package for annotation of genetic variants") - (description "This R package can annotate variants, compute amino acid -coding changes and predict coding outcomes.") - (license license:artistic2.0))) - (define-public r-limma (package (name "r-limma")