gnu: Add codingquarry.

* gnu/packages/bioinformatics.scm (codingquarry): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
This commit is contained in:
Rob Syme 2016-03-11 11:47:24 +08:00 committed by Leo Famulari
parent 8e14e059c4
commit 6a35566df7
1 changed files with 40 additions and 0 deletions

View File

@ -958,6 +958,46 @@ also includes an interface for tabix.")
"CLIPper is a tool to define peaks in CLIP-seq datasets.") "CLIPper is a tool to define peaks in CLIP-seq datasets.")
(license license:gpl2))) (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 (define-public couger
(package (package
(name "couger") (name "couger")