* [PATCH] Add more genomes.
@ 2016-04-06 15:34 Ricardo Wurmus
2016-04-06 19:11 ` Leo Famulari
0 siblings, 1 reply; 2+ messages in thread
From: Ricardo Wurmus @ 2016-04-06 15:34 UTC (permalink / raw)
To: guix-devel
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: 0001-gnu-Add-r-bsgenome-mmusculus-ucsc-mm9.patch --]
[-- Type: text/x-patch, Size: 2227 bytes --]
From 8cf38d1a43af8d89578e0604156d5097c88a212f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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.
---
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
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0002-gnu-Add-r-bsgenome-celegans-ucsc-ce6.patch --]
[-- Type: text/x-patch, Size: 2280 bytes --]
From 71eb33921e7179e04800554c775a321e1ecca297 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #3: 0003-gnu-Add-r-bsgenome-dmelanogaster-ucsc-dm3.patch --]
[-- Type: text/x-patch, Size: 2267 bytes --]
From 6c2e98a5754c9959765774f8ef10feed6cbc1dbd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
^ permalink raw reply related [flat|nested] 2+ messages in thread
* Re: [PATCH] Add more genomes.
2016-04-06 15:34 [PATCH] Add more genomes Ricardo Wurmus
@ 2016-04-06 19:11 ` Leo Famulari
0 siblings, 0 replies; 2+ messages in thread
From: Leo Famulari @ 2016-04-06 19:11 UTC (permalink / raw)
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 <ricardo.wurmus@mdc-berlin.de>
> 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 <ricardo.wurmus@mdc-berlin.de>
> 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 <ricardo.wurmus@mdc-berlin.de>
> 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
>
^ permalink raw reply [flat|nested] 2+ messages in thread
end of thread, other threads:[~2016-04-06 19:11 UTC | newest]
Thread overview: 2+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2016-04-06 15:34 [PATCH] Add more genomes Ricardo Wurmus
2016-04-06 19:11 ` Leo Famulari
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/guix.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).