Re: [PATCH] gnu: Include CodingQuarry gene predictor

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

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Dear Guix,

I have attached the amended patch to add the CodingQuarry gene predictor
(v2.0). Thanks for the kind feedback on my previous patch. I have tried to
make the formatting etc look as close as I can to the other GNU patches,
but let me know if I've missed anything.

Rob Syme
Research Associate
Pulse Pathology and Genetics
Centre for Crop and Disease Management
Curtin University


On Thu, 10 Mar 2016 at 01:59 Andreas Enge <andreas@enge.fr> wrote:

> On Tue, Mar 08, 2016 at 06:39:37PM -0500, Leo Famulari wrote:
> > > +         (delete 'check) ;; Don't run the 'make check' step of the
> > > gnu-build-system
> > When skippping the tests, we prefer to say why in the comment. It can be
> > as simple as "no test suite" if that is the case.
>
> And use in the argument block:
> #:tests? #f
> instead of deleting the phase.
>
> Andreas
>
>

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From 8cc815999e4481d45e503faa77e06053204385f8 Mon Sep 17 00:00:00 2001
From: Rob Syme <rob.syme@gmail.com>
Date: Fri, 11 Mar 2016 11:47:24 +0800
Subject: [PATCH] gnu: Add CodingQuarry.

* gnu/packages/bioinformatics.scm (codingquarry): New variable.
---
 gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b3d8827..aec16f3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -957,6 +957,49 @@ 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")))
+               (mkdir-p bin)
+               (mkdir-p doc)
+               (copy-file "INSTRUCTIONS.pdf"
+                          (string-append doc "/INSTRUCTIONS.pdf"))
+               (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")
-- 
2.5.0