Packaging UCSC

Packaging UCSC

[Pjotr Prins]

Anyone got UCSC running with Guix? May be easier than Galaxy which is
also on the books at some point.

Pj.

Re: Packaging UCSC

[zimoun]

Hi Pjotr,

On Thu, 27 Feb 2020 at 19:22, Pjotr Prins <pjotr.public12@thebird.nl> wrote:

> Anyone got UCSC running with Guix? May be easier than Galaxy which is
> also on the books at some point.

You are talking about that [1], right?
But is it free software? I am not able to find the license and [2] is
not very helpful...

[1] http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads
[2] http://genome.ucsc.edu/license/


Cheers,
simon

Re: Packaging UCSC

[Giovanni Biscuolo]

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Hi,

zimoun <zimon.toutoune@gmail.com> writes:

> Hi Pjotr,
>
> On Thu, 27 Feb 2020 at 19:22, Pjotr Prins <pjotr.public12@thebird.nl> wrote:
>
>> Anyone got UCSC running with Guix? May be easier than Galaxy which is
>> also on the books at some point.

Just a curiosity: I'm completely ignorant on this tools but are UCSC
Genome Browser and Galaxy in the same category?

AFAIU UCSC Genome Browser in "just" a browser [1] while Galaxy is a
"workflow management system" [2] (GWL is missing, and that _is_ the
solution to the workflow problem space :-) )

Is Galaxy also capable of genome browsing?

> You are talking about that [1], right?
> But is it free software?

Unfortunately not

> I am not able to find the license and [2] is
> not very helpful...
>
> [1] http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads

I know it's not a proper license attribution, but the very first
sentence in "Source and utilities downloads" states:

--8<---------------cut here---------------start------------->8---

The source for the Genome Browser, Blat, liftOver and other utilities is
free for non-profit academic research and for personal use. For
information on commercial licensing, see the Genome Browser and Blat
licensing requirements. The source and executables for several of these
products can be downloaded or purchased from our online store.

--8<---------------cut here---------------end--------------->8---

To download the source code you have to buy it
https://genome-store.ucsc.edu/
and on checkout there is this option:

--8<---------------cut here---------------start------------->8---

During checkout, non-profit academic users will be given the option to
declare that they are not using the products commercially and qualify
for a free license.

--8<---------------cut here---------------end--------------->8---

Source code is free like free beer.

> [2] http://genome.ucsc.edu/license/

This page also points to the EULA
http://genome.ucsc.edu/license/gbLicense2019.pdf

HTH, Gio'

[1] https://en.wikipedia.org/wiki/Genome_browser

[2] https://en.wikipedia.org/wiki/Bioinformatics_workflow_management_system

-- 
Giovanni Biscuolo

Xelera IT Infrastructures

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Re: Packaging UCSC

[zimoun]

Hi Giovanni,

> AFAIU UCSC Genome Browser in "just" a browser [1] while Galaxy is a
> "workflow management system" [2] (GWL is missing, and that _is_ the
> solution to the workflow problem space :-) )
>
> Is Galaxy also capable of genome browsing?

Nothing I am aware of. But I am not an real Galaxy user.

Note that GWL and Galaxy are not exactly in the same "problem space";
mainly because Galaxy is a monster hairy beast. ;-)
Well, it depends on which level the comparison is done. Galaxy is
based on visual "graphical programming" and IMHO that said a lot about
the "problem space".


> > You are talking about that [1], right?
> > But is it free software?
>
> Unfortunately not

[...]

> This page also points to the EULA
> http://genome.ucsc.edu/license/gbLicense2019.pdf

Thank you for having looked into it.


Cheers,
simon

Re: Packaging UCSC

[Pjotr Prins]

On Fri, Feb 28, 2020 at 10:12:28AM +0100, Giovanni Biscuolo wrote:
> Is Galaxy also capable of genome browsing?

Not that I am aware. There may be some SNP browsing tools in Galaxy.

> --8<---------------cut here---------------start------------->8---
> 
> The source for the Genome Browser, Blat, liftOver and other utilities is
> free for non-profit academic research and for personal use. For
> information on commercial licensing, see the Genome Browser and Blat
> licensing requirements. The source and executables for several of these
> products can be downloaded or purchased from our online store.
> 
> --8<---------------cut here---------------end--------------->8---

It is good that it is pointed out on this list. Thank you.

Pj.

Re: Packaging UCSC

[Ricardo Wurmus]

Pjotr Prins <pjotr.public12@thebird.nl> writes:

> Anyone got UCSC running with Guix? May be easier than Galaxy which is
> also on the books at some point.

Most of the UCSC browser is non-free software.  The kentutils make up a
part of the code.  Some of the kentutils are free software and are
available in Guix as the “kentutils” package.

-- 
Ricardo

Re: Packaging UCSC

[Pjotr Prins]

On Fri, Feb 28, 2020 at 02:20:16PM +0100, Ricardo Wurmus wrote:
> 
> Pjotr Prins <pjotr.public12@thebird.nl> writes:
> 
> > Anyone got UCSC running with Guix? May be easier than Galaxy which is
> > also on the books at some point.
> 
> Most of the UCSC browser is non-free software.  The kentutils make up a
> part of the code.  Some of the kentutils are free software and are
> available in Guix as the “kentutils” package.

Ouch. Thanks all for pointing this out. I'll start poking about the
license.

Pj.