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authorBen Woodcroft <donttrustben@gmail.com>2016-01-16 13:33:08 +1000
committerBen Woodcroft <donttrustben@gmail.com>2016-01-25 08:35:11 +1000
commitbcadaf00504ef467319475756a1c0516f600bf11 (patch)
tree58fd27b518befe5fa4238e8f9daf2ff97916633b /gnu
parent74273b6f2d5c39a61d9ec12827c4c018723cdf76 (diff)
downloadpatches-bcadaf00504ef467319475756a1c0516f600bf11.tar
patches-bcadaf00504ef467319475756a1c0516f600bf11.tar.gz
gnu: Add sortmerna.
* gnu/packages/bioinformatics.scm (sortmerna): New variable.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm43
1 files changed, 43 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c8eb2b8ec4..a9df676fc6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3141,6 +3141,49 @@ 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)
+ (outputs '("out" ;for binaries
+ "db")) ;for sequence databases
+ (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"))
+ (db (assoc-ref outputs "db"))
+ (share
+ (string-append db "/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 of next generation
+sequencing (NGS) 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")