From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add genome annotations. Date: Tue, 16 Feb 2016 17:25:49 +0100 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:39804) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aViRv-0004Rq-Lv for guix-devel@gnu.org; Tue, 16 Feb 2016 11:26:05 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aViRq-0004lJ-Kx for guix-devel@gnu.org; Tue, 16 Feb 2016 11:26:03 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:39584) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aViRp-0004l0-Vi for guix-devel@gnu.org; Tue, 16 Feb 2016 11:25:58 -0500 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 76700380F05 for ; Tue, 16 Feb 2016 17:25:56 +0100 (CET) Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id zRoH2Z-vAAcf for ; Tue, 16 Feb 2016 17:25:50 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Tue, 16 Feb 2016 17:25:50 +0100 (CET) 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@gnu.org" --=-=-= Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi Guix, here are four patches to add genome annotation packages for R. The species names (=E2=80=9CMouse=E2=80=9D, =E2=80=9CWorm=E2=80=9D, =E2=80=9C= Human=E2=80=9D, =E2=80=9CFly=E2=80=9D) are capitalised because they refer to the names of common model organisms. ~~ Ricardo PS: for the curious: =E2=80=9Chs=E2=80=9D =3D =E2=80=9CHomo sapiens=E2=80= =9D (human), =E2=80=9Cce=E2=80=9D =3D =E2=80=9CCaenorhabditis elegans=E2=80=9D (worm), =E2=80=9Cdm=E2=80=9D =3D= =E2=80=9CDrosophila melanogaster=E2=80=9D (fly), =E2=80=9Cmm=E2=80=9D =3D =E2=80=9CMus musculus=E2=80=9D (mouse). --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-r-org-hs-eg-db.patch" >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 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0002-gnu-Add-r-org-ce-eg-db.patch" >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 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0003-gnu-Add-r-org-dm-eg-db.patch" >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 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0004-gnu-Add-r-org-mm-eg-db.patch" >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 --=-=-=--