Re: [PATCH] gnu: Add kallisto.

[Ra <ilpuccio.febo@gmail.com>]

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Hi Alex,

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

> Hello,
>
>
> Looking at the license text:
>
> Copyright ©2015. The Regents of the University of California (Regents). All
> Rights Reserved. Permission to use, copy, modify, and distribute this
> software
> 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
> 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 <ilpuccio.febo@gmail.com> 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 <ilpuccio.febo@gmail.com>
> > 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)))
>

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