custom.scm

(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")))
               (mkdir-p bin)
               (copy-file "CodingQuarry"
                          (string-append bin "/CodingQuarry"))
               (copy-file "CufflinksGTF_to_CodingQuarryGFF3.py"
                          (string-append bin "/CufflinksGTF_to_CodingQuarryGFF3.py"))
               (copy-recursively "QuarryFiles"
                                 (string-append out "/QuarryFiles"))))))))
    (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.
Version 2 includes a special pathogen-mode (CodingQuarry-PM) that assists in
the prediction of effectors in fungal phytopathogen species.")
    (home-page "https://sourceforge.net/projects/codingquarry/")
    (license license:gpl3+)))

(define-public codingquarry-1.3
  (package (inherit codingquarry)
    (name "codingquarry-1.3")
    (version "1.3")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "mirror://sourceforge/codingquarry/CodingQuarry_v"
                    version ".tar.gz"))
              (sha256
               (base32
                "1nicv9k7g7w7c7zihr27xa27xnrd46p6n3b801hh13a7d5775fzi"))))
    (build-system gnu-build-system)
    (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+)))