[PATCH] gnu: Add kallisto.

[PATCH] gnu: Add kallisto.

[Ra]

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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

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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)))
-- 
1.9.1

Re: [PATCH] gnu: Add kallisto.

[Alex Vong]

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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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Re: [PATCH] gnu: Add kallisto.

[Ra]

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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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Re: [PATCH] gnu: Add kallisto.

[Marius Bakke]

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

> I should find a way to have a different branch/repo for "special" packages.

It is easy to use a third-party repository with Guix. Just export the
variable GUIX_PACKAGE_PATH to point to the repository as described here:

https://www.gnu.org/software/guix/manual/guix.html#Package-Modules

See e.g. these repositories for examples:

https://github.com/BIMSBbioinfo/guix-bimsb
https://github.com/MRC-CLIMB/guix-climb

Hope this helps!

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Re: [PATCH] gnu: Add kallisto.

[Ricardo Wurmus]

Alex Vong <alexvong1995@gmail.com> writes:

> 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).

Correct.  Kallisto is non-free software.

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

I don’t know of any version that is free software.

-- 
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

Re: [PATCH] gnu: Add kallisto.

[Ra]

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Hi Ricardo,

On Wed, Jan 18, 2017 at 9:31 PM Ricardo Wurmus <rekado@elephly.net> wrote:

>
> Alex Vong <alexvong1995@gmail.com> writes:
>
> > 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).
>
> Correct.  Kallisto is non-free software.
>
> > Does anybody know of any fork or should we use an old version?
>
> I don’t know of any version that is free software.
>

Looking around, I saw that you are using Kallisto at BIMSB and you have
other software I need (latest rsem);  Other software I want to work/port to
guix are https://github.com/tderrien/FEELnc,
https://github.com/Teichlab/tracer ( and Trinity). Does it make sense to
contribute to https://github.com/BIMSBbioinfo/ or do you suggest to go with
a personal/independent repo ?

--
Ra


> --
> Ricardo
>
> GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
> https://elephly.net
>
>

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Re: [PATCH] gnu: Add kallisto.

[Ricardo Wurmus]

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

> Other software I want to work/port to
> guix are https://github.com/tderrien/FEELnc,

This appears to be free software under GPL.

> https://github.com/Teichlab/tracer

And this is free software under ASL2.0.

> Does it make sense to
> contribute to https://github.com/BIMSBbioinfo/ or do you suggest to go with
> a personal/independent repo ?

You are welcome to contribute to BIMSBbioinfo, especially somewhat
unusual variants to free bioinformatics software that is in Guix
upstream.

Note that everything in staging.scm should eventually be upstreamed, so
it doesn’t make much sense to add things there.  Instead packages should
be contributed directly to Guix.

--
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net