[PATCH] Add r-bsgenome-hsapiens-ucsc-hg19.

[PATCH] Add r-bsgenome-hsapiens-ucsc-hg19.

[Ricardo Wurmus]

[-- Attachment #1: Type: text/plain, Size: 27 bytes --]

Behold: the human genome!


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-Add-r-bsgenome-hsapiens-ucsc-hg19.patch --]
[-- Type: text/x-patch, Size: 2216 bytes --]

From d4ea9fc93f18c7949ad87b980b0e8a5e03f91c00 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 18 Mar 2016 12:15:50 +0100
Subject: [PATCH] gnu: Add r-bsgenome-hsapiens-ucsc-hg19.

* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19): 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 b119fd2..7692361 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4796,6 +4796,37 @@ plots the corresponding sequence logo as introduced by Schneider and
 Stephens (1990).")
     (license license:lgpl2.0+)))
 
+(define-public r-bsgenome-hsapiens-ucsc-hg19
+  (package
+    (name "r-bsgenome-hsapiens-ucsc-hg19")
+    (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.Hsapiens.UCSC.hg19_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
+    (properties
+     `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
+    (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.Hsapiens.UCSC.hg19/")
+    (synopsis "Full genome sequences for Homo sapiens")
+    (description
+     "This package provides full genome sequences for Homo sapiens as provided
+by UCSC (hg19, February 2009) and stored in Biostrings objects.")
+    (license license:artistic2.0)))
+
 (define-public r-qtl
  (package
   (name "r-qtl")
-- 
2.1.0

Re: [PATCH] Add r-bsgenome-hsapiens-ucsc-hg19.

[Leo Famulari]

On Wed, Apr 06, 2016 at 05:32:29PM +0200, Ricardo Wurmus wrote:
> Behold: the human genome!

> +    (license license:artistic2.0)))

What a strange turn of events, that a human genome is copyrighted!
Anyways, I don't see any problems with the package.