[PATCH] Add more genomes.

[Ricardo Wurmus]

>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.
---
 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