From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH 25/25] gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene. Date: Wed, 21 Sep 2016 22:45:41 +0200 Message-ID: <20160921204541.3981-25-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]:48958) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bmoRk-0000Q2-P2 for guix-devel@gnu.org; Wed, 21 Sep 2016 16:48:52 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bmoRi-0003Dm-Mq for guix-devel@gnu.org; Wed, 21 Sep 2016 16:48:47 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:56074) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bmoRi-0003DO-Gk for guix-devel@gnu.org; Wed, 21 Sep 2016 16:48:46 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id EEE2C41B889 for ; Wed, 21 Sep 2016 22:48:45 +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 9KjgbbxK278S for ; Wed, 21 Sep 2016 22:48:40 +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 22:48:40 +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-txdb-hsapiens-ucsc-hg19-knowngene): New variable. --- gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 07a5ff6..346d7a8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5415,6 +5415,38 @@ annotation infrastructure.") "This package provides a pipeline for the analysis of GRO-seq data.") (license license:gpl3+))) +(define-public r-txdb-hsapiens-ucsc-hg19-knowngene + (package + (name "r-txdb-hsapiens-ucsc-hg19-knowngene") + (version "3.2.2") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "http://bioconductor.org/packages/" + "release/data/annotation/src/contrib" + "/TxDb.Hsapiens.UCSC.hg19.knownGene_" + version ".tar.gz")) + (sha256 + (base32 + "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) + (properties + `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) + (build-system r-build-system) + ;; As this package provides little more than a very large data file it + ;; doesn't make sense to build substitutes. + (arguments `(#:substitutable? #f)) + (propagated-inputs + `(("r-genomicfeatures" ,r-genomicfeatures))) + (home-page + "http://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") + (synopsis "Annotation package for human genome in TxDb format") + (description + "This package provides an annotation database of Homo sapiens genome +data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" +track. The database is exposed as a @code{TxDb} object.") + (license license:artistic2.0))) + (define-public vsearch (package (name "vsearch") -- 2.9.3