* [PATCH] Add genome annotations.
@ 2016-02-16 16:25 Ricardo Wurmus
2016-02-20 5:49 ` Leo Famulari
2016-02-20 12:41 ` Ben Woodcroft
0 siblings, 2 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2016-02-16 16:25 UTC (permalink / raw)
To: guix-devel@gnu.org
[-- Attachment #1: Type: text/plain, Size: 438 bytes --]
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.
~~ Ricardo
PS: for the curious: “hs” = “Homo sapiens” (human), “ce” =
“Caenorhabditis elegans” (worm), “dm” = “Drosophila melanogaster” (fly),
“mm” = “Mus musculus” (mouse).
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[-- Attachment #2: 0001-gnu-Add-r-org-hs-eg-db.patch --]
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From f0ed886cb4399d8acd15e6fa894042f60a0a4bcd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #3: 0002-gnu-Add-r-org-ce-eg-db.patch --]
[-- Type: text/x-patch, Size: 1905 bytes --]
From 2c56640fcefc3f2d3cd5d855fe0c716d79e1f45f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #4: 0003-gnu-Add-r-org-dm-eg-db.patch --]
[-- Type: text/x-patch, Size: 1868 bytes --]
From 8b7925f69c6cd69a62407990707be094e0997536 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #5: 0004-gnu-Add-r-org-mm-eg-db.patch --]
[-- Type: text/x-patch, Size: 1870 bytes --]
From 3e07a3c07423754852d82c909447508d41f28c30 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
^ permalink raw reply related [flat|nested] 4+ messages in thread
* Re: [PATCH] Add genome annotations.
2016-02-16 16:25 [PATCH] Add genome annotations Ricardo Wurmus
@ 2016-02-20 5:49 ` Leo Famulari
2016-02-20 12:41 ` Ben Woodcroft
1 sibling, 0 replies; 4+ messages in thread
From: Leo Famulari @ 2016-02-20 5:49 UTC (permalink / raw)
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 <ricardo.wurmus@mdc-berlin.de>
> 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 <ricardo.wurmus@mdc-berlin.de>
> 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 <ricardo.wurmus@mdc-berlin.de>
> 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 <ricardo.wurmus@mdc-berlin.de>
> 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
>
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH] Add genome annotations.
2016-02-16 16:25 [PATCH] Add genome annotations Ricardo Wurmus
2016-02-20 5:49 ` Leo Famulari
@ 2016-02-20 12:41 ` Ben Woodcroft
2016-02-24 16:27 ` Ricardo Wurmus
1 sibling, 1 reply; 4+ messages in thread
From: Ben Woodcroft @ 2016-02-20 12:41 UTC (permalink / raw)
To: Ricardo Wurmus, guix-devel@gnu.org
On 17/02/16 02:25, 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.
Thanks for this Ricardo. My only comment is that perhaps the
descriptions could be a little less shorthand, something like
"This package provides mappings from Entrez gene identifiers to various
+annotations for genome of the model worm Caernorhabditis elegans.")
and similar for Drosophila and mouse. There is only one human species,
so OK there.
ben
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH] Add genome annotations.
2016-02-20 12:41 ` Ben Woodcroft
@ 2016-02-24 16:27 ` Ricardo Wurmus
0 siblings, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2016-02-24 16:27 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel@gnu.org
Ben Woodcroft <b.woodcroft@uq.edu.au> writes:
> On 17/02/16 02:25, 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.
>
> Thanks for this Ricardo. My only comment is that perhaps the
> descriptions could be a little less shorthand, something like
>
> "This package provides mappings from Entrez gene identifiers to various
> +annotations for genome of the model worm Caernorhabditis elegans.")
>
>
> and similar for Drosophila and mouse. There is only one human species,
> so OK there.
I made them a little more explicit for mouse, worm, and fruit fly.
Thanks!
~~ Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2016-02-24 16:27 UTC | newest]
Thread overview: 4+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2016-02-16 16:25 [PATCH] Add genome annotations Ricardo Wurmus
2016-02-20 5:49 ` Leo Famulari
2016-02-20 12:41 ` Ben Woodcroft
2016-02-24 16:27 ` Ricardo Wurmus
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