* 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
