From mboxrd@z Thu Jan 1 00:00:00 1970 From: Rob Syme Subject: Re: [PATCH] gnu: Include CodingQuarry gene predictor Date: Wed, 16 Mar 2016 08:51:16 +0000 Message-ID: References: <20160308233937.GB24107@jasmine> <20160309175902.GB30271@solar> <20160316085023.GA14979@jasmine> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=047d7bdc190c7e1c5d052e269ec8 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:54770) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ag7Av-0007H1-Or for guix-devel@gnu.org; Wed, 16 Mar 2016 04:51:31 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ag7Au-0002wi-5t for guix-devel@gnu.org; Wed, 16 Mar 2016 04:51:29 -0400 Received: from mail-ig0-x233.google.com ([2607:f8b0:4001:c05::233]:34543) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ag7At-0002wY-VK for guix-devel@gnu.org; Wed, 16 Mar 2016 04:51:28 -0400 Received: by mail-ig0-x233.google.com with SMTP id av4so109126947igc.1 for ; Wed, 16 Mar 2016 01:51:27 -0700 (PDT) In-Reply-To: <20160316085023.GA14979@jasmine> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Leo Famulari Cc: guix-devel@gnu.org --047d7bdc190c7e1c5d052e269ec8 Content-Type: text/plain; charset=UTF-8 Thanks! On Wed, 16 Mar 2016 at 16:50 Leo Famulari 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 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 > > 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 > > > > --047d7bdc190c7e1c5d052e269ec8 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Thanks!=C2=A0

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 predict= or
> (v2.0). Thanks for the kind feedback on my previous patch. I have trie= d to
> make the formatting etc look as close as I can to the other GNU patche= s,
> 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:
> > > > +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(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 commen= t. It can be
> > > as simple as "no test suite" if that is the case.<= br> > >
> > 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.
> ---
>=C2=A0 gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++= ++++++++++++++
>=C2=A0 1 file changed, 43 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinforma= tics.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.")
>=C2=A0 =C2=A0 =C2=A0 =C2=A0"CLIPper is a tool to define peaks in C= LIP-seq datasets.")
>=C2=A0 =C2=A0 =C2=A0 (license license:gpl2)))
>
> +(define-public codingquarry
> +=C2=A0 (package
> +=C2=A0 =C2=A0 (name "codingquarry")
> +=C2=A0 =C2=A0 (version "2.0")
> +=C2=A0 =C2=A0 (source (origin
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (method url-fetch) > +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (uri (string-append<= br> > +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= "mirror://sourceforge/codingquarry/CodingQuarry_v"
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= version ".tar.gz"))
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (sha256
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(base32
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 "0115hkj= flsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
> +=C2=A0 =C2=A0 (build-system gnu-build-system)
> +=C2=A0 =C2=A0 (arguments
> +=C2=A0 =C2=A0 =C2=A0'(#:tests? #f ; no "check" target > +=C2=A0 =C2=A0 =C2=A0 =C2=A0#:phases
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0(modify-phases %standard-phases
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(delete 'configure)
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(replace 'install
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(lambda* (#:key outputs #:al= low-other-keys)
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(let* ((out (assoc-re= f outputs "out"))
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= (bin (string-append out "/bin"))
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= (doc (string-append out "/share/doc/codingquarry")))
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(mkdir-p bin)<= br> > +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(mkdir-p doc)<= br> > +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(copy-file &qu= ot;INSTRUCTIONS.pdf"
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 (string-append doc "/INSTRUCTIONS.pdf")) > +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(copy-recursiv= ely "QuarryFiles"
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(string-append out "/= QuarryFiles"))
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(install-file = "CodingQuarry" bin)
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(install-file = "CufflinksGTF_to_CodingQuarryGFF3.py" bin)))))))
> +=C2=A0 =C2=A0 (inputs `(("openmpi" ,openmpi)))
> +=C2=A0 =C2=A0 (native-search-paths
> +=C2=A0 =C2=A0 =C2=A0(list (search-path-specification
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (variable "QUARRY_PATH= ")
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (files '("QuarryFi= les")))))
> +=C2=A0 =C2=A0 (native-inputs `(("python" ,python-2))) ; Onl= y Python 2 is supported
> +=C2=A0 =C2=A0 (synopsis "Fungal gene predictor")
> +=C2=A0 =C2=A0 (description "CodingQuarry is a highly accurate, s= elf-training GHMM fungal
> +gene predictor designed to work with assembled, aligned RNA-seq trans= cripts.")
> +=C2=A0 =C2=A0 (home-page "https://sourcefor= ge.net/projects/codingquarry/")
> +=C2=A0 =C2=A0 (license license:gpl3+)))
> +
>=C2=A0 (define-public couger
>=C2=A0 =C2=A0 (package
>=C2=A0 =C2=A0 =C2=A0 (name "couger")
> --
> 2.5.0
>

--047d7bdc190c7e1c5d052e269ec8--