From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: guix-devel <guix-devel@gnu.org>
Subject: [PATCH] Add more genomes.
Date: Wed, 6 Apr 2016 17:34:37 +0200 [thread overview]
Message-ID: <idjd1q2699u.fsf@bimsb-sys02.mdc-berlin.net> (raw)
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[-- 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
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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
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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
next reply other threads:[~2016-04-06 15:34 UTC|newest]
Thread overview: 2+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-04-06 15:34 Ricardo Wurmus [this message]
2016-04-06 19:11 ` [PATCH] Add more genomes Leo Famulari
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