Thanks in advance as usual.
>From 448c2435e50d9d860f1153934058effa42fc6495 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <[email protected]>
Date: Sat, 16 Jan 2016 13:33:08 +1000
Subject: [PATCH] gnu: Add sortmerna.
* gnu/packages/bioinformatics.scm (sortmerna): New variable.
---
gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e579afe..e170ff7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3016,6 +3016,45 @@ optimized for modern read lengths of 100 bases or higher, and takes advantage
of these reads to align data quickly through a hash-based indexing scheme.")
(license license:asl2.0)))
+(define-public sortmerna
+ (package
+ (name "sortmerna")
+ (version "2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/biocore/sortmerna/archive/";
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1670a92x1vvkacnvgr2i5xac3ls6lp4pc3n0bccnmllsnymggcf0"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (share (string-append out "/share/sortmerna/rRNA_databases")))
+ (install-file "sortmerna" bin)
+ (install-file "indexdb_rna" bin)
+ (for-each (lambda (file)
+ (install-file file share))
+ (find-files "rRNA_databases" ".*fasta"))
+ #t))))))
+ (home-page "http://bioinfo.lifl.fr/RNA/sortmerna";)
+ (synopsis "Biological sequence analysis tool for NGS reads")
+ (description
+ "SortMeRNA is a biological sequence analysis tool for filtering, mapping
+and operational taxonomic unit (OTU) picking next generation sequencing reads.
+The core algorithm is based on approximate seeds and allows for fast and
+sensitive analyses of nucleotide sequences. The main application of SortMeRNA
+is filtering rRNA from metatranscriptomic data.")
+ (license license:lgpl3)))
+
(define-public star
(package
(name "star")
--
2.6.3
