From aa3eeeb5420524a2ba23b8484534cefe5ab181a9 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 30 Jan 2017 12:11:04 +0100
Subject: gnu: Add r-bsgenome-hsapiens-1000genomes-hs37d5.

* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
  New variable.
---
 gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3bf352193c..c605c58ea6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6885,6 +6885,37 @@ dependencies between GO terms can be implemented and applied.")
 genome data packages and support for efficient SNP representation.")
     (license license:artistic2.0)))
 
+(define-public r-bsgenome-hsapiens-1000genomes-hs37d5
+  (package
+    (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
+    (version "0.99.1")
+    (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.1000genomes.hs37d5_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
+    (properties
+     `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
+    (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.1000genomes.hs37d5/")
+    (synopsis "Full genome sequences for Homo sapiens")
+    (description
+     "This package provides full genome sequences for Homo sapiens from
+1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
+    (license license:artistic2.0)))
+
 (define-public r-impute
   (package
     (name "r-impute")
-- 
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