From mboxrd@z Thu Jan 1 00:00:00 1970 From: Leo Famulari Subject: Re: [PATCH] Add more genomes. Date: Wed, 6 Apr 2016 15:11:33 -0400 Message-ID: <20160406191133.GC6333@jasmine> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:45546) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ansra-0004oe-9j for guix-devel@gnu.org; Wed, 06 Apr 2016 15:11:39 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ansrW-000076-6b for guix-devel@gnu.org; Wed, 06 Apr 2016 15:11:38 -0400 Received: from out5-smtp.messagingengine.com ([66.111.4.29]:51016) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ansrW-00006s-2O for guix-devel@gnu.org; Wed, 06 Apr 2016 15:11:34 -0400 Received: from compute3.internal (compute3.nyi.internal [10.202.2.43]) by mailout.nyi.internal (Postfix) with ESMTP id EDCC920FA1 for ; Wed, 6 Apr 2016 15:11:33 -0400 (EDT) Content-Disposition: inline In-Reply-To: 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: Ricardo Wurmus Cc: guix-devel On Wed, Apr 06, 2016 at 05:34:37PM +0200, Ricardo Wurmus wrote: > 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. LGTM! > --- > 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 > > 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 > > 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 >