From mboxrd@z Thu Jan 1 00:00:00 1970 From: Leo Famulari Subject: Re: [PATCH] Add genome annotations. Date: Sat, 20 Feb 2016 00:49:27 -0500 Message-ID: <20160220054927.GA9159@jasmine> References: Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:58556) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aX0QB-0001DV-Az for guix-devel@gnu.org; Sat, 20 Feb 2016 00:49:36 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aX0Q7-0000t8-69 for guix-devel@gnu.org; Sat, 20 Feb 2016 00:49:35 -0500 Received: from out3-smtp.messagingengine.com ([66.111.4.27]:60359) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aX0Q7-0000t4-1u for guix-devel@gnu.org; Sat, 20 Feb 2016 00:49:31 -0500 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@gnu.org" On Tue, Feb 16, 2016 at 05:25:49PM +0100, Ricardo Wurmus wrote: > Hi Guix, > > here are four patches to add genome annotation packages for R. The > species names (“Mouse”, “Worm”, “Human”, “Fly”) are capitalised because > they refer to the names of common model organisms. "Genome wide annotation for Worm" Heh :) These are my favorite synopses in Guix. Or, they will be when you please push! > > ~~ Ricardo > > PS: for the curious: “hs” = “Homo sapiens” (human), “ce” = > “Caenorhabditis elegans” (worm), “dm” = “Drosophila melanogaster” (fly), > “mm” = “Mus musculus” (mouse). > > From f0ed886cb4399d8acd15e6fa894042f60a0a4bcd Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Wed, 13 Jan 2016 16:27:29 +0100 > Subject: [PATCH 1/4] gnu: Add r-org-hs-eg-db. > > * gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable. > --- > gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ > 1 file changed, 26 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 9b5bd12..fe82329 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -4330,6 +4330,32 @@ genomic feature data as long as it has minimal information on the locations of > genomic intervals. In addition, it can use BAM or BigWig files as input.") > (license license:artistic2.0))) > > +(define-public r-org-hs-eg-db > + (package > + (name "r-org-hs-eg-db") > + (version "3.2.3") > + (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/" > + "org.Hs.eg.db_" version ".tar.gz")) > + (sha256 > + (base32 > + "0xicgkbh6xkvs74s1piafqac63dyz2ycdyil4pj4ghhxx2sabm6p")))) > + (properties > + `((upstream-name . "org.Hs.eg.db"))) > + (build-system r-build-system) > + (propagated-inputs > + `(("r-annotationdbi" ,r-annotationdbi))) > + (home-page "http://www.bioconductor.org/packages/org.Hs.eg.db/") > + (synopsis "Genome wide annotation for Human") > + (description > + "This package provides mappings from Entrez gene identifiers to various > +annotations for the human genome.") > + (license license:artistic2.0))) > + > (define-public r-qtl > (package > (name "r-qtl") > -- > 2.1.0 > > From 2c56640fcefc3f2d3cd5d855fe0c716d79e1f45f Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Tue, 16 Feb 2016 17:19:30 +0100 > Subject: [PATCH 2/4] gnu: Add r-org-ce-eg-db. > > * gnu/packages/bioinformatics.scm (r-org-ce-eg-db): New variable. > --- > gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ > 1 file changed, 26 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index fe82329..79f5309 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -4356,6 +4356,32 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") > annotations for the human genome.") > (license license:artistic2.0))) > > +(define-public r-org-ce-eg-db > + (package > + (name "r-org-ce-eg-db") > + (version "3.2.3") > + (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/" > + "org.Ce.eg.db_" version ".tar.gz")) > + (sha256 > + (base32 > + "1d0lx00ybq34yqs6mziaa0lrh77xm0ggsmi76g6k95f77gi7m1sw")))) > + (properties > + `((upstream-name . "org.Ce.eg.db"))) > + (build-system r-build-system) > + (propagated-inputs > + `(("r-annotationdbi" ,r-annotationdbi))) > + (home-page "http://www.bioconductor.org/packages/org.Ce.eg.db/") > + (synopsis "Genome wide annotation for Worm") > + (description > + "This package provides mappings from Entrez gene identifiers to various > +annotations for the C. elegans genome.") > + (license license:artistic2.0))) > + > (define-public r-qtl > (package > (name "r-qtl") > -- > 2.1.0 > > From 8b7925f69c6cd69a62407990707be094e0997536 Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Tue, 16 Feb 2016 17:19:55 +0100 > Subject: [PATCH 3/4] gnu: Add r-org-dm-eg-db. > > * gnu/packages/bioinformatics.scm (r-org-dm-eg-db): New variable. > --- > gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ > 1 file changed, 26 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 79f5309..deaef00 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -4382,6 +4382,32 @@ annotations for the human genome.") > annotations for the C. elegans genome.") > (license license:artistic2.0))) > > +(define-public r-org-dm-eg-db > + (package > + (name "r-org-dm-eg-db") > + (version "3.2.3") > + (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/" > + "org.Dm.eg.db_" version ".tar.gz")) > + (sha256 > + (base32 > + "0mib46c7nr00l7mh290n383za9hyl91a1dc6jhjbk884jmxaxyz6")))) > + (properties > + `((upstream-name . "org.Dm.eg.db"))) > + (build-system r-build-system) > + (propagated-inputs > + `(("r-annotationdbi" ,r-annotationdbi))) > + (home-page "http://www.bioconductor.org/packages/org.Dm.eg.db/") > + (synopsis "Genome wide annotation for Fly") > + (description > + "This package provides mappings from Entrez gene identifiers to various > +annotations for the fruit fly genome.") > + (license license:artistic2.0))) > + > (define-public r-qtl > (package > (name "r-qtl") > -- > 2.1.0 > > From 3e07a3c07423754852d82c909447508d41f28c30 Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Tue, 16 Feb 2016 17:20:32 +0100 > Subject: [PATCH 4/4] gnu: Add r-org-mm-eg-db. > > * gnu/packages/bioinformatics.scm (r-org-mm-eg-db): New variable. > --- > gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ > 1 file changed, 26 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index deaef00..623eeb6 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -4408,6 +4408,32 @@ annotations for the C. elegans genome.") > annotations for the fruit fly genome.") > (license license:artistic2.0))) > > +(define-public r-org-mm-eg-db > + (package > + (name "r-org-mm-eg-db") > + (version "3.2.3") > + (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/" > + "org.Mm.eg.db_" version ".tar.gz")) > + (sha256 > + (base32 > + "0wh1pm3npdg7070875kfgiid3bqkz3q7rq6snhk6bxfvph00298y")))) > + (properties > + `((upstream-name . "org.Mm.eg.db"))) > + (build-system r-build-system) > + (propagated-inputs > + `(("r-annotationdbi" ,r-annotationdbi))) > + (home-page "http://www.bioconductor.org/packages/org.Mm.eg.db/") > + (synopsis "Genome wide annotation for Mouse") > + (description > + "This package provides mappings from Entrez gene identifiers to various > +annotations for the mouse genome.") > + (license license:artistic2.0))) > + > (define-public r-qtl > (package > (name "r-qtl") > -- > 2.1.0 >