[PATCH] gnu: Include CodingQuarry gene predictor

[Rob Syme <rob.syme@gmail.com>]

* gnu/packages/bioinformatics.scm: Add codingquarry package description
---
 gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5d53dc9..2e665db 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -914,6 +914,37 @@ 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 "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)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'check) ;; Don't run the 'make check' step of the
gnu-build-system
+         (replace 'install ;; Replace the install step with the
function defined below
+           (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"))))))))
+    (inputs `(("openmpi", openmpi)))
+    (native-inputs `(("python", python-2)))
+    (synopsis "CodingQuarry is a highly accurate, self-training GHMM
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 licence:gpl3+)))
+
 (define-public couger
   (package
     (name "couger")
-- 
2.5.0