From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add more genomes. Date: Wed, 6 Apr 2016 17:34:37 +0200 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:35514) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1anpTn-0004v6-3a for guix-devel@gnu.org; Wed, 06 Apr 2016 11:34:52 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1anpTh-0007YL-0N for guix-devel@gnu.org; Wed, 06 Apr 2016 11:34:51 -0400 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:55832) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1anpTg-0007Y9-Mo for guix-devel@gnu.org; Wed, 06 Apr 2016 11:34:44 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id 2A9CF28096C for ; Wed, 6 Apr 2016 17:34:44 +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 N0oHGSJosbIl for ; Wed, 6 Apr 2016 17:34:37 +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 17:34:37 +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/x-patch Content-Disposition: inline; filename="0001-gnu-Add-r-bsgenome-mmusculus-ucsc-mm9.patch" >From 8cf38d1a43af8d89578e0604156d5097c88a212f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 30 Mar 2016 12:23:51 +0200 Subject: [PATCH 1/3] gnu: Add r-bsgenome-mmusculus-ucsc-mm9. * gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9): 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 9532e38..fd99ac4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4943,6 +4943,37 @@ Stephens (1990).") by UCSC (hg19, February 2009) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-bsgenome-mmusculus-ucsc-mm9 + (package + (name "r-bsgenome-mmusculus-ucsc-mm9") + (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.Mmusculus.UCSC.mm9_" + version ".tar.gz")) + (sha256 + (base32 + "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) + (properties + `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) + (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.Mmusculus.UCSC.mm9/") + (synopsis "Full genome sequences for Mouse") + (description + "This package provides full genome sequences for Mus musculus (Mouse) as +provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") + (license license:artistic2.0))) + (define-public r-motifrg (package (name "r-motifrg") -- 2.1.0 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0002-gnu-Add-r-bsgenome-celegans-ucsc-ce6.patch" >From 71eb33921e7179e04800554c775a321e1ecca297 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 30 Mar 2016 12:24:16 +0200 Subject: [PATCH 2/3] gnu: Add r-bsgenome-celegans-ucsc-ce6. * gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6): 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 fd99ac4..2fb1182 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4974,6 +4974,38 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.") provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-bsgenome-celegans-ucsc-ce6 + (package + (name "r-bsgenome-celegans-ucsc-ce6") + (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.Celegans.UCSC.ce6_" + version ".tar.gz")) + (sha256 + (base32 + "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) + (properties + `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) + (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.Celegans.UCSC.ce6/") + (synopsis "Full genome sequences for Worm") + (description + "This package provides full genome sequences for Caenorhabditis +elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings +objects.") + (license license:artistic2.0))) + (define-public r-motifrg (package (name "r-motifrg") -- 2.1.0 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0003-gnu-Add-r-bsgenome-dmelanogaster-ucsc-dm3.patch" >From 6c2e98a5754c9959765774f8ef10feed6cbc1dbd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 30 Mar 2016 12:24:44 +0200 Subject: [PATCH 3/3] gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3. * gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3): 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 2fb1182..01e9060 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5006,6 +5006,38 @@ elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-bsgenome-dmelanogaster-ucsc-dm3 + (package + (name "r-bsgenome-dmelanogaster-ucsc-dm3") + (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.Dmelanogaster.UCSC.dm3_" + version ".tar.gz")) + (sha256 + (base32 + "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) + (properties + `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) + (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.Dmelanogaster.UCSC.dm3/") + (synopsis "Full genome sequences for Fly") + (description + "This package provides full genome sequences for Drosophila +melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in +Biostrings objects.") + (license license:artistic2.0))) + (define-public r-motifrg (package (name "r-motifrg") -- 2.1.0 --=-=-=--