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Re: [PATCH] Add genome annotations.
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From: |
Leo Famulari |
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Subject: |
Re: [PATCH] Add genome annotations. |
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Date: |
Sat, 20 Feb 2016 00:49:27 -0500 |
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User-agent: |
Mutt/1.5.24 (2015-08-30) |
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 <address@hidden>
> 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 <address@hidden>
> 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 <address@hidden>
> 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 <address@hidden>
> 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
>