From 63daca1e927136d184f41ebdd9b01923d1ee3bff Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Sun, 26 Apr 2020 21:33:42 +0200
Subject: gnu: Add r-snplocs-hsapiens-dbsnp144-grch37.

* gnu/packages/bioconductor.scm (r-snplocs-hsapiens-dbsnp144-grch37): New
  variable.
---
 gnu/packages/bioconductor.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a27845581f..b5fa77655c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6466,6 +6466,44 @@ and parameters of which are trained on a set of aligned reads and a reference
 genome sequence.")
     (license license:lgpl3)))
 
+(define-public r-snplocs-hsapiens-dbsnp144-grch37
+  (package
+    (name "r-snplocs-hsapiens-dbsnp144-grch37")
+    (version "0.99.20")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
+                                     version 'annotation))
+              (sha256
+               (base32
+                "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
+    (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-biocgenerics" ,r-biocgenerics)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-iranges" ,r-iranges)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-biostrings" ,r-biostrings)))
+    (home-page
+     "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
+    (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
+    (description "This package provides SNP locations and alleles for Homo
+sapiens extracted from NCBI dbSNP Build 144.  The source data files used for
+this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
+to reference genome GRCh37.p13.  Note that the GRCh37.p13 genome is a
+patched version of GRCh37.  However the patch doesn't alter chromosomes 1-22,
+X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
+the mitochondrion chromosome.  Therefore, the SNPs in this package can be
+injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
+correct position but this injection will exclude chrM (i.e. nothing will be
+injected in that sequence).")
+    (license license:artistic2.0)))
+
 (define-public r-reqon
   (package
     (name "r-reqon")
-- 
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