From: Leo Famulari <leo@famulari.name>
To: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Cc: guix-devel <guix-devel@gnu.org>
Subject: Re: [PATCH] Add more genomes.
Date: Wed, 6 Apr 2016 15:11:33 -0400 [thread overview]
Message-ID: <20160406191133.GC6333@jasmine> (raw)
In-Reply-To: <idjd1q2699u.fsf@bimsb-sys02.mdc-berlin.net>
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
>
prev parent reply other threads:[~2016-04-06 19:11 UTC|newest]
Thread overview: 2+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-04-06 15:34 [PATCH] Add more genomes Ricardo Wurmus
2016-04-06 19:11 ` Leo Famulari [this message]
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=20160406191133.GC6333@jasmine \
--to=leo@famulari.name \
--cc=guix-devel@gnu.org \
--cc=ricardo.wurmus@mdc-berlin.de \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this external index
https://git.savannah.gnu.org/cgit/guix.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.