@@ 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")