From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id SEnPK4OWX18DMQAA0tVLHw (envelope-from ) for ; Mon, 14 Sep 2020 16:12:51 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1 with LMTPS id 0Ec1JoOWX1+cbgAAbx9fmQ (envelope-from ) for ; Mon, 14 Sep 2020 16:12:51 +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 0A7FB940878 for ; Mon, 14 Sep 2020 16:12:51 +0000 (UTC) Received: from localhost ([::1]:56142 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kHr61-0000At-Ua for larch@yhetil.org; Mon, 14 Sep 2020 12:12:49 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:55176) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kHr2N-0004OG-8M for guix-patches@gnu.org; Mon, 14 Sep 2020 12:09:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:44449) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kHr2M-0002e8-SH for guix-patches@gnu.org; Mon, 14 Sep 2020 12:09:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kHr2M-0008U3-NM for guix-patches@gnu.org; Mon, 14 Sep 2020 12:09:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move to (gnu packages bioconductor). References: <20200914160414.7572-1-zimon.toutoune@gmail.com> In-Reply-To: <20200914160414.7572-1-zimon.toutoune@gmail.com> Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 14 Sep 2020 16:09:02 +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=B43400.160009968332421 (code B ref 43400); Mon, 14 Sep 2020 16:09:02 +0000 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:03 +0000 Received: from localhost ([127.0.0.1]:55966 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1O-0008QR-8q for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:03 -0400 Received: from mail-wr1-f51.google.com ([209.85.221.51]:38544) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1M-0008Pj-8I for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:00 -0400 Received: by mail-wr1-f51.google.com with SMTP id g4so260476wrs.5 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:00 -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=Si/ab2uYi+yX7lgCqvxxVrMZR9akjslFB91Jum1G8K0=; b=lUrfLzKT8WBvBomdNY3RPWTYHCIPXgd16JL6KFQgyXzhiG3tn0eOaL9rCxhhLQ7vAI omkodIpFPq+rsOr9rl9XvDvR0m0SO7iNJ/05zW4mDRxDktPDLh5dZbijW8w/H+mh+I4G O8fR6hOuyt2dTBs6PYGW+UxRMoC7lZG3IBMn0iaLgWvtcCldJXyf+yHLUPpcfithK6dJ t+b/xqZkQEkvJ0EToAfPlJpR2TCTVpah9FhgU7tCGhTMh8pM94Pk/ZVzhqBysVjNYr4T WqUWyltm423oc0VkapTWUCRFI4eGBKnX/+geU7fXQ8BIyQq6zRrZjyl6P5uOWSuDR1k9 MMxQ== 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=Si/ab2uYi+yX7lgCqvxxVrMZR9akjslFB91Jum1G8K0=; b=LpwMwZxbVqenihVlwBdZp0ovyS9PH3vTp1PUt9KvFoslV83Ri+Wq4IxX57eR+/USKf 7dEMcLC9U5XR3/u8t25qH9yRyweNNlWjunMi09e5n50KZFRowzD4rDSJ5ZPbMVlgKlvN usNMEfnWegog5S8wfrrSvaWHlP18d7vrRKWuKPK/+hgOicJ/PL9FfAG/sxUHNFeO1X54 OIfUO2uGN+pe7UZsY/ck+JqHPvSsuwGHtOHsnT6mZQeucqj4H7dqzsrFWSX7QXXM+SDF bpbapMlI3d0OWVmMOy8fWeVsVrq8k61702faFE9D5G5mZ2yjIKmgYZGhqeuCDDDRdsYV EL5w== X-Gm-Message-State: AOAM531jSx+bX4uf4UsvyZMBBcymrzNLozEY/i9EmDddDLc7OLx45an6 5exNCl8uEv4iRlVVDDHKNWlWT72Ild0= X-Google-Smtp-Source: ABdhPJxrUsv0dNOkmyUDj7vRcqaelPywADa7sFwnpMQZK5oD3EvmaogFeGhiIsum4Pmb2csljyqleg== X-Received: by 2002:a05:6000:1083:: with SMTP id y3mr16503811wrw.405.1600099674004; Mon, 14 Sep 2020 09:07:54 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.07.53 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:07:53 -0700 (PDT) From: zimoun Date: Mon, 14 Sep 2020 18:07:36 +0200 Message-Id: <20200914160747.8983-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 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=lUrfLzKT; 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: 0.09 X-TUID: t7Bkj3p413sG * gnu/packages/cran.scm (r-fourcseq): Move from here... * gnu/packages/bioconductor.scm (r-fourcseq): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++ gnu/packages/cran.scm | 44 ---------------------------------- 2 files changed, 45 insertions(+), 44 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index db1fdcad17..01c4748500 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019 Simon Tournier ;;; Copyright © 2020 Peter Lo +;;; Copyright © 2020 Mădălin Ionel Patrașcu ;;; ;;; This file is part of GNU Guix. ;;; @@ -8241,3 +8242,47 @@ with: @end itemize ") (license license:gpl2+))) + +(define-public r-fourcseq + (package + (name "r-fourcseq") + (version "1.22.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "FourCSeq" version)) + (sha256 + (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b")))) + (properties `((upstream-name . "FourCSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biostrings" ,r-biostrings) + ("r-deseq2" ,r-deseq2) + ("r-fda" ,r-fda) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggbio" ,r-ggbio) + ("r-ggplot2" ,r-ggplot2) + ("r-gtools" ,r-gtools) + ("r-lsd" ,r-lsd) + ("r-matrix" ,r-matrix) + ("r-reshape2" ,r-reshape2) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") + (synopsis "Analysis of multiplexed 4C sequencing data") + (description + "This package is an R package dedicated to the analysis of (multiplexed) +4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific +interactions between DNA elements and identify differential interactions +between conditions. The statistical analysis in R starts with individual bam +files for each sample as inputs. To obtain these files, the package contains +a Python script to demultiplex libraries and trim off primer sequences. With +a standard alignment software the required bam files can be then be +generated.") + (license license:gpl3+))) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index be66533b0b..1ba763ff66 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22572,50 +22572,6 @@ Try a demo of the LSD by running @code{demotour()}.") ;; Either version (license (list license:gpl2 license:gpl3)))) -(define-public r-fourcseq - (package - (name "r-fourcseq") - (version "1.22.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "FourCSeq" version)) - (sha256 - (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b")))) - (properties `((upstream-name . "FourCSeq"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-deseq2" ,r-deseq2) - ("r-fda" ,r-fda) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-gtools" ,r-gtools) - ("r-lsd" ,r-lsd) - ("r-matrix" ,r-matrix) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page - "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") - (synopsis "Analysis of multiplexed 4C sequencing data") - (description - "This package is an R package dedicated to the analysis of (multiplexed) -4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific -interactions between DNA elements and identify differential interactions -between conditions. The statistical analysis in R starts with individual bam -files for each sample as inputs. To obtain these files, the package contains -a Python script to demultiplex libraries and trim off primer sequences. With -a standard alignment software the required bam files can be then be -generated.") - (license license:gpl3+))) - (define-public r-phylogram (package (name "r-phylogram") -- 2.28.0