From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ra Subject: Re: [PATCH] gnu: Add kallisto. Date: Wed, 18 Jan 2017 17:58:32 +0000 Message-ID: References: <87eg00mxp4.fsf@gmail.com> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=94eb2c075040d00ee70546622afe Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:40873) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cTuVR-0005pH-QS for guix-devel@gnu.org; Wed, 18 Jan 2017 12:58:48 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cTuVP-0000yW-Pb for guix-devel@gnu.org; Wed, 18 Jan 2017 12:58:45 -0500 Received: from mail-yw0-x233.google.com ([2607:f8b0:4002:c05::233]:34133) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1cTuVP-0000x2-Ig for guix-devel@gnu.org; Wed, 18 Jan 2017 12:58:43 -0500 Received: by mail-yw0-x233.google.com with SMTP id w75so13730801ywg.1 for ; Wed, 18 Jan 2017 09:58:43 -0800 (PST) In-Reply-To: <87eg00mxp4.fsf@gmail.com> 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" To: Alex Vong Cc: guix-devel --94eb2c075040d00ee70546622afe Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Alex, On Wed, Jan 18, 2017 at 12:09 PM Alex Vong wrote: > Hello, > > > Looking at the license text: > > Copyright =C2=A92015. The Regents of the University of California (Regent= s). All > Rights Reserved. Permission to use, copy, modify, and distribute this > software > and its documentation for educational and research not-for-profit purpose= s, > without fee and without a signed licensing agreement, is hereby granted, > provided that the above copyright notice, this paragraph and the followin= g > two > paragraphs appear in all copies, modifications, and distributions. Contac= t > The > Office of Technology Licensing, UC Berkeley, 2150 Shattuck Avenue, Suite > 510, > Berkeley, CA 94720-1620, (510) 643-7201, for commercial licensing > opportunities. > > > It seems the license is {fsf, dfsg} non-free because it does not allow > commercial usage. More precisely, it violates freedom 0 (the freedom to > run the program as you wish, for any purpose). > > > Does anybody know of any fork or should we use an old version? > > Do you mean that this package can not be included or I need to fall back to an older version ? In both cases, I should find a way to have a different branch/repo for "special" packages. -- Ra > > Cheers, > Alex > > > Ra writes: > > > Hi, > > I think I need your help to identify the right license for this package= , > I set bsd-3 only for > > convenience this is the original license > > (https://github.com/pachterlab/kallisto/blob/master/license.txt) > > > > Do I need to use something like : > > (license (license:non-copyleft "file://src/COPYING" > > "See src/COPYING in the > distribution.")))) > > > > * gnu/packages/bioinformatics.scm (kallisto): New variable. > > --- > > gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++ > > 1 file changed, 28 insertions(+) > > > > diff --git a/gnu/packages/bioinformatics.scm > b/gnu/packages/bioinformatics.scm > > index c60bedc..86026fd 100644 > > --- a/gnu/packages/bioinformatics.scm > > +++ b/gnu/packages/bioinformatics.scm > > @@ -8502,3 +8502,31 @@ a specified false discovery rate. It also > contains a number of utilities > > to > > explore the MS/MS results and assess missed and irregular enzymatic > cleavages, > > mass measurement accuracy, etc.") > > (license license:artistic2.0))) > > + > > +(define-public kallisto > > + (package > > + (name "kallisto") > > + (version "0.43.0") > > + (source (origin > > + (method url-fetch) > > + (uri (string-append > > + "https://github.com/pachterlab/kallisto/archive/v" > > + version ".tar.gz")) > > + (file-name (string-append name "-" version ".tar.gz")) > > + (sha256 > > + (base32 > > + "1d9cqf3lz6mm9kmqn47d99c6byn6q9l4ppgcafxrhcnrb2davhv9")))) > > + (build-system cmake-build-system) > > + (arguments > > + '(#:tests? #f)) ; no "check" target > > + (inputs > > + `(("zlib" ,zlib) > > + ("hdf5" ,hdf5))) > > + (home-page "https://pachterlab.github.io/kallisto") > > + (synopsis "Near-optimal RNA-Seq quantification") > > + (description > > + "Kallisto is a program for quantifying abundances of transcripts from > > +RNA-Seq data, or more generally of target sequences using > high-throughput > > +sequencing reads. It is based on the novel idea of pseudoalignment for > rapidly > > +determining the compatibility of reads with targets, without the need > for alignment.") > > + (license license:bsd-3))) > > -- > > 1.9.1 > > > > From f30c6b20e2564f3617ab3dde40af10bfbe790749 Mon Sep 17 00:00:00 2001 > > From: Raoul Jean Pierre Bonnal > > Date: Wed, 18 Jan 2017 10:46:49 +0100 > > Subject: [PATCH] gnu: Add kallisto. > > > > * gnu/packages/bioinformatics.scm (kallisto): New variable. > > --- > > gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++ > > 1 file changed, 28 insertions(+) > > > > diff --git a/gnu/packages/bioinformatics.scm > b/gnu/packages/bioinformatics.scm > > index c60bedc..86026fd 100644 > > --- a/gnu/packages/bioinformatics.scm > > +++ b/gnu/packages/bioinformatics.scm > > @@ -8502,3 +8502,31 @@ a specified false discovery rate. It also > contains a number of utilities to > > explore the MS/MS results and assess missed and irregular enzymatic > cleavages, > > mass measurement accuracy, etc.") > > (license license:artistic2.0))) > > + > > +(define-public kallisto > > + (package > > + (name "kallisto") > > + (version "0.43.0") > > + (source (origin > > + (method url-fetch) > > + (uri (string-append > > + "https://github.com/pachterlab/kallisto/archive/v" > > + version ".tar.gz")) > > + (file-name (string-append name "-" version ".tar.gz")) > > + (sha256 > > + (base32 > > + > "1d9cqf3lz6mm9kmqn47d99c6byn6q9l4ppgcafxrhcnrb2davhv9")))) > > + (build-system cmake-build-system) > > + (arguments > > + '(#:tests? #f)) ; no "check" target > > + (inputs > > + `(("zlib" ,zlib) > > + ("hdf5" ,hdf5))) > > + (home-page "https://pachterlab.github.io/kallisto") > > + (synopsis "Near-optimal RNA-Seq quantification") > > + (description > > + "Kallisto is a program for quantifying abundances of transcripts > from > > +RNA-Seq data, or more generally of target sequences using > high-throughput > > +sequencing reads. It is based on the novel idea of pseudoalignment for > rapidly > > +determining the compatibility of reads with targets, without the need > for alignment.") > > + (license license:bsd-3))) > --94eb2c075040d00ee70546622afe Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Alex,

On Wed, Jan 18, 2017 at 12:09 PM Alex Vong <alexvong1995@gmail.com> wrote:
Hello,


Looking at the license text:

Copyright =C2=A92015. The Regents of the University of California (Regents)= . All
Rights Reserved. Permission to use, copy, modify, and distribute this softw= are
and its documentation for educational and research not-for-profit purposes,=
without fee and without a signed licensing agreement, is hereby granted, provided that the above copyright notice, this paragraph and the following = two
paragraphs appear in all copies, modifications, and distributions. Contact = The
Office of Technology Licensing, UC Berkeley, 2150 Shattuck Avenue, Suite 51= 0,
Berkeley, CA 94720-1620, (510) 643-7201, for commercial licensing
opportunities.


It seems the license is {fsf, dfsg} non-free because it does not allow
commercial usage. More precisely, it violates freedom 0 (the freedom to
run the program as you wish, for any purpose).


Does anybody know of any fork or should we use an old version?


Do you mean that t= his package can not be included or I need to fall back to an older version = ?=C2=A0 In both cases, I should find a way to have a different branch/repo = for "special" packages.=C2=A0

--
Ra


=C2=A0

Cheers,
Alex


Ra <ilpuccio.febo@gmail.com> writes:

> Hi,
> I think I need your help to identify the right license for this packag= e, I set bsd-3 only for
> convenience this is the original license
> (https://gith= ub.com/pachterlab/kallisto/blob/master/license.txt)
>
> Do I need to use something like :
> (license (license:non-copyleft "file://src/COPYING"
>=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 =C2=A0 "See src/COPYI= NG in the distribution."))))
>
> * gnu/packages/bioinformatics.scm (kallisto): New variable.
> ---
> gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
> 1 file changed, 28 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinforma= tics.scm
> index c60bedc..86026fd 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -8502,3 +8502,31 @@ a specified false discovery rate. It also conta= ins a number of utilities
> to
> explore the MS/MS results and assess missed and irregular enzymatic cl= eavages,
> mass measurement accuracy, etc.")
> (license license:artistic2.0)))
> +
> +(define-public kallisto
> + (package
> + (name "kallisto")
> + (version "0.43.0")
> + (source (origin
> + (method url-fetch)
> + (uri (string-append
> + "https://github.com/= pachterlab/kallisto/archive/v"
> + version ".tar.gz"))
> + (file-name (string-append name "-" version ".tar.gz&q= uot;))
> + (sha256
> + (base32
> + "1d9cqf3lz6mm9kmqn47d99c6byn6q9l4ppgcafxrhcnrb2davhv9"))))=
> + (build-system cmake-build-system)
> + (arguments
> + '(#:tests? #f)) ; no "check" target
> + (inputs
> + `(("zlib" ,zlib)
> + ("hdf5" ,hdf5)))
> + (home-page "https://pachterlab.= github.io/kallisto")
> + (synopsis "Near-optimal RNA-Seq quantification")
> + (description
> + "Kallisto is a program for quantifying abundances of transcript= s from
> +RNA-Seq data, or more generally of target sequences using high-throug= hput
> +sequencing reads. It is based on the novel idea of pseudoalignment fo= r rapidly
> +determining the compatibility of reads with targets, without the need= for alignment.")
> + (license license:bsd-3)))
> --
> 1.9.1
>
> From f30c6b20e2564f3617ab3dde40af10bfbe790749 Mon Sep 17 00:00:00 2001=
> From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com&g= t;
> Date: Wed, 18 Jan 2017 10:46:49 +0100
> Subject: [PATCH] gnu: Add kallisto.
>
> * gnu/packages/bioinformatics.scm (kallisto): New variable.
> ---
>=C2=A0 gnu/packages/bioinformatics.scm | 28 +++++++++++++++++++++++++++= +
>=C2=A0 1 file changed, 28 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinforma= tics.scm
> index c60bedc..86026fd 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -8502,3 +8502,31 @@ a specified false discovery rate.=C2=A0 It also= contains a number of utilities to
>=C2=A0 explore the MS/MS results and assess missed and irregular enzyma= tic cleavages,
>=C2=A0 mass measurement accuracy, etc.")
>=C2=A0 =C2=A0 =C2=A0 (license license:artistic2.0)))
> +
> +(define-public kallisto
> +=C2=A0 (package
> +=C2=A0 =C2=A0 (name "kallisto")
> +=C2=A0 =C2=A0 (version "0.43.0")
> +=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 class=3D"gmail_msg"> > +=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= "https://github.com/pachte= rlab/kallisto/archive/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 (file-name (string-a= ppend name "-" 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 "1d9cqf3= lz6mm9kmqn47d99c6byn6q9l4ppgcafxrhcnrb2davhv9"))))
> +=C2=A0 =C2=A0 (build-system cmake-build-system)
> +=C2=A0 =C2=A0 (arguments
> +=C2=A0 =C2=A0 =C2=A0'(#:tests? #f)) ; no "check" target=
> +=C2=A0 =C2=A0 (inputs
> +=C2=A0 =C2=A0 =C2=A0`(("zlib" ,zlib)
> +=C2=A0 =C2=A0 =C2=A0 =C2=A0("hdf5" ,hdf5)))
> +=C2=A0 =C2=A0 (home-page "https:= //pachterlab.github.io/kallisto")
> +=C2=A0 =C2=A0 (synopsis "Near-optimal RNA-Seq quantification&quo= t;)
> +=C2=A0 =C2=A0 (description
> +=C2=A0 =C2=A0 =C2=A0"Kallisto is a program for quantifying abund= ances of transcripts from
> +RNA-Seq data, or more generally of target sequences using high-throug= hput
> +sequencing reads. It is based on the novel idea of pseudoalignment fo= r rapidly
> +determining the compatibility of reads with targets, without the need= for alignment.")
> +=C2=A0 =C2=A0 (license license:bsd-3)))
--94eb2c075040d00ee70546622afe--