From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add r-bsgenome-hsapiens-ucsc-hg19. Date: Wed, 6 Apr 2016 17:32:29 +0200 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:34921) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1anpRg-0004Ds-O0 for guix-devel@gnu.org; Wed, 06 Apr 2016 11:32:44 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1anpRd-00075Y-Dy for guix-devel@gnu.org; Wed, 06 Apr 2016 11:32:40 -0400 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:55820) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1anpRd-00075S-3P for guix-devel@gnu.org; Wed, 06 Apr 2016 11:32:37 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id 57FF2280AC2 for ; Wed, 6 Apr 2016 17:32:36 +0200 (CEST) Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id FqPwonx-W_Op for ; Wed, 6 Apr 2016 17:32:30 +0200 (CEST) Received: from HTCATWO.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 sinope.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Wed, 6 Apr 2016 17:32:30 +0200 (CEST) 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-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel --=-=-= Content-Type: text/plain Behold: the human genome! --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-r-bsgenome-hsapiens-ucsc-hg19.patch" >From d4ea9fc93f18c7949ad87b980b0e8a5e03f91c00 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 18 Mar 2016 12:15:50 +0100 Subject: [PATCH] gnu: Add r-bsgenome-hsapiens-ucsc-hg19. * gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19): New variable. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b119fd2..7692361 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4796,6 +4796,37 @@ plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).") (license license:lgpl2.0+))) +(define-public r-bsgenome-hsapiens-ucsc-hg19 + (package + (name "r-bsgenome-hsapiens-ucsc-hg19") + (version "1.4.0") + (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://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "BSgenome.Hsapiens.UCSC.hg19_" + version ".tar.gz")) + (sha256 + (base32 + "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) + (properties + `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) + (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-bsgenome" ,r-bsgenome))) + (home-page + "http://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") + (synopsis "Full genome sequences for Homo sapiens") + (description + "This package provides full genome sequences for Homo sapiens as provided +by UCSC (hg19, February 2009) and stored in Biostrings objects.") + (license license:artistic2.0))) + (define-public r-qtl (package (name "r-qtl") -- 2.1.0 --=-=-=--