01/01: gnu: Add r-txdb-mmusculus-ucsc-mm10-knowngene.

[Roel Janssen]

roelj pushed a commit to branch master
in repository guix.

commit c5173d74d67b786c36dd53930c5d4fe4805cf3e9
Author: Roel Janssen <address@hidden>
Date:   Thu Jan 12 10:02:57 2017 +0100

    gnu: Add r-txdb-mmusculus-ucsc-mm10-knowngene.
    
    * gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): 
New variable.
---
 gnu/packages/bioinformatics.scm |   35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 14daf59..d82b6c0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7100,6 +7100,41 @@ musculus (Mouse) as provided by UCSC (mm10, December 
2011) and stored
 in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
+  (package
+    (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
+    (version "3.4.0")
+    (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/"
+                                  "TxDb.Mmusculus.UCSC.mm10.knownGene_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb"))))
+    (properties
+     `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
+    (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)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-annotationdbi" ,r-annotationdbi)))
+    (home-page
+     "http://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/";)
+    (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
+    (description
+     "This package loads a TxDb object, which is an R interface to
+prefabricated databases contained in this package.  This package provides
+the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
+based on the knownGene track.")
+    (license license:artistic2.0)))
+
 (define-public r-bsgenome-celegans-ucsc-ce6
   (package
     (name "r-bsgenome-celegans-ucsc-ce6")