Re: [PATCH] gnu: Include CodingQuarry gene predictor

[Leo Famulari <leo@famulari.name>]

On Fri, Mar 11, 2016 at 03:55:47AM +0000, Rob Syme wrote:
> 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.

Thanks!

I simplified the install phase a little bit. Install-file does mkdir-p
for you, so I removed some extraneous parts.

Pushed as 6a35566df7

> 
> 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
> >
> >

> 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
>