Re: [PATCH] gnu: Include CodingQuarry gene predictor

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

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Thanks!

On Wed, 16 Mar 2016 at 16:50 Leo Famulari <leo@famulari.name> wrote:

> 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
> >
>
>

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