@@ 958,6 958,46 @@ also includes an interface for tabix.")
"CLIPper is a tool to define peaks in CLIP-seq datasets.")
(license license:gpl2)))
+(define-public codingquarry
+ (package
+ (name "codingquarry")
+ (version "2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "mirror://sourceforge/codingquarry/CodingQuarry_v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ; no "check" target
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (doc (string-append out "/share/doc/codingquarry")))
+ (install-file "INSTRUCTIONS.pdf" doc)
+ (copy-recursively "QuarryFiles"
+ (string-append out "/QuarryFiles"))
+ (install-file "CodingQuarry" bin)
+ (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)))))))
+ (inputs `(("openmpi" ,openmpi)))
+ (native-search-paths
+ (list (search-path-specification
+ (variable "QUARRY_PATH")
+ (files '("QuarryFiles")))))
+ (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported
+ (synopsis "Fungal gene predictor")
+ (description "CodingQuarry is a highly accurate, self-training GHMM fungal
+gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
+ (home-page "https://sourceforge.net/projects/codingquarry/")
+ (license license:gpl3+)))
+
(define-public couger
(package
(name "couger")