diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 48 |
1 files changed, 48 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bdd44128fb..4740b20da8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") |