Re: [PATCH] Add more genomes.

[Leo Famulari]

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 <address@hidden>
> 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 <address@hidden>
> 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 <address@hidden>
> 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
>