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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Mar 2021 17:59:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47010 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47010@debbugs.gnu.org Cc: zimoun Received: via spool by 47010-submit@debbugs.gnu.org id=B47010.161522630510237 (code B ref 47010); Mon, 08 Mar 2021 17:59:02 +0000 Received: (at 47010) by debbugs.gnu.org; 8 Mar 2021 17:58:25 +0000 Received: from localhost ([127.0.0.1]:44756 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9A-0002er-Ox for submit@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:25 -0500 Received: from mail-wr1-f52.google.com ([209.85.221.52]:42231) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK98-0002e3-Py for 47010@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:23 -0500 Received: by mail-wr1-f52.google.com with SMTP id j2so12399412wrx.9 for <47010@debbugs.gnu.org>; Mon, 08 Mar 2021 09:58:22 -0800 (PST) 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=IOmillYLLCiuQhvwD9JiBVbndlo/RW1bstyP2Nn3cl8=; b=Iaw0OI0M9RgRmbYhqpoeOlCKkqSxVTTnL6VeW89wSpiXTYq83wsQ+lqjy7a/24iJu0 3oUi4Ba5HYk2MpETfjj1ONdQrrYkxG+fZ6okbbioCgXc6HZsfI51xRFL1v+8UsBVqq0u mdbbAXeWjktAeBZrRbN7c5QKO43IeovdAfIWkpggCT0rsSPSIYjJN9erh20d24Zo7Y7Z 7p0ft4+EtH/1Kmctz+iL0g73WiXU/5q5tzc1WAw6LwSXpkk+PCMd0g9xtkus92T1mcf6 UPPZ2OgNa1qpQjAUeHi4qvb8sfuh20uzN0OwVBzuISs40ca8WoKK9q83mhi/nB3egNid ftTg== 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=IOmillYLLCiuQhvwD9JiBVbndlo/RW1bstyP2Nn3cl8=; b=knFshe2oriEJ1M921MDnoJcSwT8TpLxW/bxvA3Tj88U31LjBnRRYjPmCv/2H1LSOVx nE509Sz7aZqP/VTHCRySaVGs83NljoJOqbhzhzOnUyku0N0sEfuerrGSPtEUe+Bxfbyi ctYSG3h+X7NwyRZziAKGx2+0r6IfpKKfZ5uqntzoQwrfV+tXo3XPOD/Y5T82QQGFT9Ee nP0yrIqFN6CXLgZVG+fQsWbkBPrRShdStoSHptMAA47wc8A+oeCjrLhL6hIS7LEkvQva ihJ2WjW9d0pNChw/HvbBfldvxujDcfWGyf1QKpayi36RPe+L8WIX3jNc+SbVGdwVMFUH yE9Q== X-Gm-Message-State: AOAM532j2Feoe5xtZvh5XxS7+CMtPndSgT8ad1i0hc3YADNQZCEcXYta OZd44RNrf6emsWkCuA4/K2KnHumU9F8= X-Google-Smtp-Source: ABdhPJzO0GafZLGyKrR8bJZZyYQm3nZKg6tCE5YbkqYHc/ojhtJjs0W3950qJTG4ronHq08AmVDaaw== X-Received: by 2002:a5d:4002:: with SMTP id n2mr14237058wrp.148.1615226297008; Mon, 08 Mar 2021 09:58:17 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id 75sm96993wma.23.2021.03.08.09.58.16 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 08 Mar 2021 09:58:16 -0800 (PST) From: zimoun Date: Mon, 8 Mar 2021 18:57:55 +0100 Message-Id: <20210308175802.62517-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210308175802.62517-1-zimon.toutoune@gmail.com> References: <20210308175802.62517-1-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-deseq2): Move from here... * gnu/packages/bioconductor.scm (r-deseq2): ...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 e15984d0e3..f2dd4bb70b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1487,6 +1487,44 @@ structure.") microarrays.") (license license:artistic2.0))) +(define-public r-deseq2 + (package + (name "r-deseq2") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DESeq2" version)) + (sha256 + (base32 + "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp")))) + (properties `((upstream-name . "DESeq2"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-genefilter" ,r-genefilter) + ("r-geneplotter" ,r-geneplotter) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-locfit" ,r-locfit) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/DESeq2") + (synopsis "Differential gene expression analysis") + (description + "This package provides functions to estimate variance-mean dependence in +count data from high-throughput nucleotide sequencing assays and test for +differential expression based on a model using the negative binomial +distribution.") + (license license:lgpl3+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 258c3ca409..64585127e6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7385,44 +7385,6 @@ includes software to ") (license license:cc0)))) -(define-public r-deseq2 - (package - (name "r-deseq2") - (version "1.30.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DESeq2" version)) - (sha256 - (base32 - "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp")))) - (properties `((upstream-name . "DESeq2"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-locfit" ,r-locfit) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/DESeq2") - (synopsis "Differential gene expression analysis") - (description - "This package provides functions to estimate variance-mean dependence in -count data from high-throughput nucleotide sequencing assays and test for -differential expression based on a model using the negative binomial -distribution.") - (license license:lgpl3+))) - (define-public r-dexseq (package (name "r-dexseq")