From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH 08/25] gnu: Add r-deseq2. Date: Wed, 21 Sep 2016 22:45:24 +0200 Message-ID: <20160921204541.3981-8-ricardo.wurmus@mdc-berlin.de> References: <20160921204541.3981-1-ricardo.wurmus@mdc-berlin.de> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:47030) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bmoPu-00075Z-5X for guix-devel@gnu.org; Wed, 21 Sep 2016 16:46:56 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bmoPs-00027F-2j for guix-devel@gnu.org; Wed, 21 Sep 2016 16:46:53 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:56054) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bmoPr-00026V-Sb for guix-devel@gnu.org; Wed, 21 Sep 2016 16:46:52 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 5627241B86A for ; Wed, 21 Sep 2016 22:46:51 +0200 (CEST) Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 2FfyZXfdTr9D for ; Wed, 21 Sep 2016 22:46:46 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Wed, 21 Sep 2016 22:46:46 +0200 (CEST) In-Reply-To: <20160921204541.3981-1-ricardo.wurmus@mdc-berlin.de> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: guix-devel@gnu.org * gnu/packages/bioinformatics.scm (r-deseq2): New variable. --- gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 18e688f..2df63ee 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5118,6 +5118,51 @@ microarrays.") high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-deseq2 + (package + (name "r-deseq2") + (version "1.12.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DESeq2" version)) + (sha256 + (base32 + "12h77f0dpi5xaj7aqf50kkyn6lq9j7bcsly1r0ffmyfcszrp1sfx")))) + (properties `((upstream-name . "DESeq2"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'link-against-armadillo + (lambda _ + (substitute* "src/Makevars" + (("PKG_LIBS =" prefix) + (string-append prefix "-larmadillo")))))))) + (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-hmisc" ,r-hmisc) + ("r-iranges" ,r-iranges) + ("r-locfit" ,r-locfit) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "http://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 vsearch (package (name "vsearch") -- 2.9.3