From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH 23/25] gnu: Add r-systempiper. Date: Wed, 21 Sep 2016 22:45:39 +0200 Message-ID: <20160921204541.3981-23-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]:48715) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bmoRb-0000Gw-02 for guix-devel@gnu.org; Wed, 21 Sep 2016 16:48:42 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bmoRW-00035c-OY for guix-devel@gnu.org; Wed, 21 Sep 2016 16:48:37 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:46641) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bmoRW-00035B-D8 for guix-devel@gnu.org; Wed, 21 Sep 2016 16:48:34 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id D47D9380457 for ; Wed, 21 Sep 2016 22:48:33 +0200 (CEST) Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id qSvWWgFFkqdW for ; Wed, 21 Sep 2016 22:48:28 +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 venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Wed, 21 Sep 2016 22:48:28 +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-systempiper): New variable. --- gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9915247..f3843dd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5343,6 +5343,52 @@ purposes. The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-systempiper + (package + (name "r-systempiper") + (version "1.6.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "systemPipeR" version)) + (sha256 + (base32 + "0s2g46a5d5bvx45i3cgmib48wf8hrniyladhm0f7kgcbfx57248m")))) + (properties `((upstream-name . "systemPipeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-batchjobs" ,r-batchjobs) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-deseq2" ,r-deseq2) + ("r-edger" ,r-edger) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-go-db" ,r-go-db) + ("r-gostats" ,r-gostats) + ("r-limma" ,r-limma) + ("r-pheatmap" ,r-pheatmap) + ("r-rjson" ,r-rjson) + ("r-rsamtools" ,r-rsamtools) + ("r-shortread" ,r-shortread) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://github.com/tgirke/systemPipeR") + (synopsis "Next generation sequencing workflow and reporting environment") + (description + "This R package provides tools for building and running automated +end-to-end analysis workflows for a wide range of @dfn{next generation +sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. +Important features include a uniform workflow interface across different NGS +applications, automated report generation, and support for running both R and +command-line software, such as NGS aligners or peak/variant callers, on local +computers or compute clusters. Efficient handling of complex sample sets and +experimental designs is facilitated by a consistently implemented sample +annotation infrastructure.") + (license license:artistic2.0))) + (define-public vsearch (package (name "vsearch") -- 2.9.3