[PATCH] gnu: Include CodingQuarry gene predictor

[PATCH] gnu: Include CodingQuarry gene predictor

[Rob Syme]

* 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

Re: [PATCH] gnu: Include CodingQuarry gene predictor

[Leo Famulari]

On Tue, Mar 08, 2016 at 05:13:34PM +0800, Rob Syme wrote:

Thank you for the patch!

> * gnu/packages/bioinformatics.scm: Add codingquarry package description

When adding packages, we have a preferred format for the commit message.
It's either the GNU changelog format or a slightly modified version (I'm
not sure). You can see a good example in commit 0e2f2aebed.

[...]

> +         (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.

[...]

> +    (native-inputs `(("python", python-2)))

If the software only works with Python 2, I prefer to say so in a
comment such as "Only Python 2 is supported." I don't think is official
policy but I find it a useful piece of information to leave for other
readers.

Can you submit a revised patch that addresses these issues?

Re: [PATCH] gnu: Include CodingQuarry gene predictor

[Rob Syme]

[-- Attachment #1: Type: text/plain, Size: 1086 bytes --]

Sure, I'll do that. Thanks for the feedback.
-r

On Wed, 9 Mar 2016, 07:40 Leo Famulari, <leo@famulari.name> wrote:

> On Tue, Mar 08, 2016 at 05:13:34PM +0800, Rob Syme wrote:
>
> Thank you for the patch!
>
> > * gnu/packages/bioinformatics.scm: Add codingquarry package description
>
> When adding packages, we have a preferred format for the commit message.
> It's either the GNU changelog format or a slightly modified version (I'm
> not sure). You can see a good example in commit 0e2f2aebed.
>
> [...]
>
> > +         (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.
>
> [...]
>
> > +    (native-inputs `(("python", python-2)))
>
> If the software only works with Python 2, I prefer to say so in a
> comment such as "Only Python 2 is supported." I don't think is official
> policy but I find it a useful piece of information to leave for other
> readers.
>
> Can you submit a revised patch that addresses these issues?
>

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Re: [PATCH] gnu: Include CodingQuarry gene predictor

[Andreas Enge]

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

Re: [PATCH] gnu: Include CodingQuarry gene predictor

[Rob Syme]

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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

Re: [PATCH] gnu: Include CodingQuarry gene predictor

[Leo Famulari]

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
> 

Re: [PATCH] gnu: Include CodingQuarry gene predictor

[Rob Syme]

[-- Attachment #1: Type: text/plain, Size: 4144 bytes --]

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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