@@ 919,6 919,54 @@ also includes an interface for tabix.")
(define-public python2-pysam
(package-with-python2 python-pysam))
+(define-public cd-hit
+ (package
+ (name "cd-hit")
+ (version "4.6.5")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/weizhongli/cdhit"
+ "/releases/download/V" version
+ "/cd-hit-v" version "-2016-0304.tar.gz"))
+ (sha256
+ (base32
+ "15db0hq38yyifwqx9b6l34z14jcq576dmjavhj8a426c18lvnhp3"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are no tests
+ #:make-flags
+ ;; Executables are copied directly to the PREFIX.
+ (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin"))
+ #:phases
+ (modify-phases %standard-phases
+ ;; No "configure" script
+ (delete 'configure)
+ ;; Remove sources of non-determinism
+ (add-after 'unpack 'be-timeless
+ (lambda _
+ (substitute* "cdhit-utility.c++"
+ ((" \\(built on \" __DATE__ \"\\)") ""))
+ (substitute* "cdhit-common.c++"
+ (("__DATE__") "\"0\"")
+ (("\", %s, \" __TIME__ \"\\\\n\", date") ""))
+ #t))
+ ;; The "install" target does not create the target directory
+ (add-before 'install 'create-target-dir
+ (lambda* (#:key outputs #:allow-other-keys)
+ (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
+ #t)))))
+ (inputs
+ `(("perl" ,perl)))
+ (home-page "http://weizhongli-lab.org/cd-hit/")
+ (synopsis "Cluster and compare protein or nucleotide sequences")
+ (description
+ "CD-HIT is a program for clustering and comparing protein or nucleotide
+sequences. CD-HIT is designed to be fast and handle extremely large
+databases.")
+ ;; The manual says: "It can be copied under the GNU General Public License
+ ;; version 2 (GPLv2)."
+ (license license:gpl2)))
+
(define-public clipper
(package
(name "clipper")