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| author | Ben Woodcroft <donttrustben@gmail.com> | 2016-01-16 13:33:08 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2016-01-25 08:35:11 +1000 |
| commit | bcadaf00504ef467319475756a1c0516f600bf11 (patch) | |
| tree | 58fd27b518befe5fa4238e8f9daf2ff97916633b /gnu | |
| parent | 74273b6f2d5c39a61d9ec12827c4c018723cdf76 (diff) | |
| download | patches-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.scm | 43 |
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") |