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| author | Ben J Woodcroft <donttrustben@gmail.com> | 2016-09-09 09:53:21 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2016-09-13 20:27:29 +1000 |
| commit | 66daf78c0a4b64e0618a9bca8c8e6c0ce28de16d (patch) | |
| tree | 94ca5c467f0ac7ff549fd5d66a942a42146ce02d | |
| parent | 6c0cd765c03de72ecd97b9222bff04c525b8bba4 (diff) | |
| download | patches-66daf78c0a4b64e0618a9bca8c8e6c0ce28de16d.tar patches-66daf78c0a4b64e0618a9bca8c8e6c0ce28de16d.tar.gz | |
gnu: Add seqtk.
* gnu/packages/bioinformatics.scm (seqtk): New variable.
| -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 3922c660bb..39a420ac3b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4586,6 +4586,49 @@ BioPython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.") (license license:gpl3))) +(define-public seqtk + (package + (name "seqtk") + (version "1.2") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/lh3/seqtk/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Remove extraneous header files, as is done in the seqtk + ;; master branch. + (for-each (lambda (file) (delete-file file)) + (list "ksort.h" "kstring.h" "kvec.h")) + #t)))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'check + ;; There are no tests, so we just run a sanity check. + (lambda _ (zero? (system* "./seqtk" "seq")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (install-file "seqtk" bin))))))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/lh3/seqtk") + (synopsis "Toolkit for processing biological sequences in FASTA/Q format") + (description + "Seqtk is a fast and lightweight tool for processing sequences in the +FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be +optionally compressed by gzip.") + (license license:expat))) + (define-public snap-aligner (package (name "snap-aligner") |