Re: [PATCH] gnu: Add kallisto.

[Alex Vong <alexvong1995@gmail.com>]

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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?


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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