From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp2 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id qG4SDtedX1/AewAA0tVLHw (envelope-from ) for ; Mon, 14 Sep 2020 16:44:07 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp2 with LMTPS id 4GpDCNedX1+kMAAAB5/wlQ (envelope-from ) for ; Mon, 14 Sep 2020 16:44:07 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id D3BFA9404D4 for ; Mon, 14 Sep 2020 16:44:06 +0000 (UTC) Received: from localhost ([::1]:42340 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kHraH-0005zr-RC for larch@yhetil.org; Mon, 14 Sep 2020 12:44:05 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:55218) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kHr2P-0004WN-VA for guix-patches@gnu.org; Mon, 14 Sep 2020 12:09:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:44456) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kHr2P-0002ew-Ih for guix-patches@gnu.org; Mon, 14 Sep 2020 12:09:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kHr2P-0008Ut-EM for guix-patches@gnu.org; Mon, 14 Sep 2020 12:09:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#43400] [PATCH 11/12] gnu: r-hitc: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 14 Sep 2020 16:09:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 43400 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 43400@debbugs.gnu.org Cc: zimoun Received: via spool by 43400-submit@debbugs.gnu.org id=B43400.160009969332521 (code B ref 43400); Mon, 14 Sep 2020 16:09:05 +0000 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:13 +0000 Received: from localhost ([127.0.0.1]:55988 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1X-0008SJ-Uv for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:12 -0400 Received: from mail-wm1-f51.google.com ([209.85.128.51]:52687) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1T-0008QM-6P for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:07 -0400 Received: by mail-wm1-f51.google.com with SMTP id q9so578065wmj.2 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:07 -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=yiBgfilDskVqsbwUlYpzifkisiJw9rRlDq9lRcXYm7k=; b=llIf/kSWPTT6XdW1SE2aMflQTSwd0b9y5dBpG1qW+h3GU4USnX8vRAx0gq6xN8zzSw rHq3fnwefxVFMdL4JoVxWuIG9yNt6FD7YiMRTRV4IUQevt8DoRsbGg6aM2Cv1yG/vbeX AIlNejputddUW+hnnHjzCuq89886StGRrkTY+c9lb3JiIBYSbYASw1b45+LKbLijSLYQ EcqBP4hkkfFrpANf54txJDcsxxT5PhmspkHaSwvkzGwi6/vB1QpPf7AEC5PlBxhls8bt iXGmkDCh/7eEINaF/x1aVCRcNfkXN/mjsc8f/t3GG9wG2Y5zyC1N5KAPVX9Z1n7JYpbm evhQ== 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=yiBgfilDskVqsbwUlYpzifkisiJw9rRlDq9lRcXYm7k=; b=oHLIpI/CPFajJWGyBU4k0fUUs9W11vzX432PohGBfVCZI4M3aJsjHK0RLAZPmTSD8t kZJOZ18BdwG6Q+Fe7xc1faWhR4Rz5s9J04uvifu5QAQaPKqbrmhK5G+ljx97TG8xydqZ KLYmt8r84mmSQO0PrIKbTdsCjvYDd/3mum5xA1kLKX84kz/AaBgtO/zTMaD9zbZSuf8x def50Zn/FSfH4Sv6OI03U4FtT3oOpZAB+n5pyN1ah/P79PKe3v7o9BwsZ7sjEzQGdNtK liu6DTUcS9ZQBfhE2PfEYOQ1wmXUp3xH09YS/9VHg1zsJVTYkdypPu2tlNd28rQMITvZ H+Xg== X-Gm-Message-State: AOAM532TF+4Ae0A/jfza/pAxLnWDuCexGd43e8KUQXPcrfgaLknHFXsA 9Tu7b1VpC/bfL8Lf7GnvNzTlJiCPO/A= X-Google-Smtp-Source: ABdhPJwbZvc28kuwYqx9H8HZ09rRhFjaINxFh6TRueqAUZ4QjYcU/9XRoc9iRMUXgm/V8FeScm6/3g== X-Received: by 2002:a05:600c:4104:: with SMTP id j4mr147137wmi.36.1600099681229; Mon, 14 Sep 2020 09:08:01 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.08.00 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:08:00 -0700 (PDT) From: zimoun Date: Mon, 14 Sep 2020 18:07:45 +0200 Message-Id: <20200914160747.8983-10-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com> References: <20200914160747.8983-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -1.0 (-) X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=fail (rsa verify failed) header.d=gmail.com header.s=20161025 header.b=llIf/kSW; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Spam-Score: 4.09 X-TUID: IWxl7kO+mwoW * gnu/packages/bioinformatics.scm (r-hitc): Move from here... * gnu/packages/bioconductor.scm (r-hitc): ...to here. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b6a09c4ce4..5878c43a3d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8337,6 +8337,35 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-hitc + (package + (name "r-hitc") + (version "1.32.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "HiTC" version)) + (sha256 + (base32 + "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy")))) + (properties `((upstream-name . "HiTC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rtracklayer" ,r-rtracklayer))) + (home-page "https://bioconductor.org/packages/HiTC") + (synopsis "High throughput chromosome conformation capture analysis") + (description + "The HiTC package was developed to explore high-throughput \"C\" data +such as 5C or Hi-C. Dedicated R classes as well as standard methods for +quality controls, normalization, visualization, and further analysis are also +provided.") + (license license:artistic2.0))) + (define-public r-hdf5array (package (name "r-hdf5array") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d874fe9a13..6bbcc3fe00 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10625,35 +10625,6 @@ intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.") (license license:gpl2+))) -(define-public r-hitc - (package - (name "r-hitc") - (version "1.32.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "HiTC" version)) - (sha256 - (base32 - "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy")))) - (properties `((upstream-name . "HiTC"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer))) - (home-page "https://bioconductor.org/packages/HiTC") - (synopsis "High throughput chromosome conformation capture analysis") - (description - "The HiTC package was developed to explore high-throughput \"C\" data -such as 5C or Hi-C. Dedicated R classes as well as standard methods for -quality controls, normalization, visualization, and further analysis are also -provided.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.28.0