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| author | Rob Syme <rob.syme@gmail.com> | 2016-03-11 11:47:24 +0800 |
|---|---|---|
| committer | Leo Famulari <leo@famulari.name> | 2016-03-16 04:49:27 -0400 |
| commit | 6a35566df7e2f9876242d10a14074ae662a0037f (patch) | |
| tree | bde622dc0605065d18dc66bb488716e9d68fef9c | |
| parent | 8e14e059c40c22b946e7beef64dc9e4d3b3d5e35 (diff) | |
gnu: Add codingquarry.
* gnu/packages/bioinformatics.scm (codingquarry): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 40 |
1 files changed, 40 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4dd2ee6f92..190a058cc6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") |