Fwd: Returning BLAST datatypes and DB loc files to Galaxy core?

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Fwd: Returning BLAST datatypes and DB loc files to Galaxy core?

Peter Cock
Dear all,

I ran this past the IUC first, and the only comments were
positive.

Although I wasn't at GCC2017 to discuss this in person,
I understand that the Galaxy Team now encourages
widely used datatypes to be included in the main Galaxy
repository, rather than distributed via the Tool Shed.

To that end, would a pull request returning the BLAST
datatypes and associated database *.loc files be welcome?

These are currently on my GitHub repository here:
https://github.com/peterjc/galaxy_blast/

And the datatypes are distributed via the Tool Shed here:
http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes

Assuming this happens, we would need to phase out the
tool shed version (but it will still be needed while older
Galaxy instances are still running).

Are there any pitfalls to worry about if the datatypes are
already there with Galaxy and the tool shed version is
installed on top? Or the tool shed version was installed
but then Galaxy was updated to include the version
bundled with Galaxy?

Thanks,

Peter
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Re: Returning BLAST datatypes and DB loc files to Galaxy core?

Peter Cock
I have a work-in-progress branch and pull request here,
https://github.com/peterjc/galaxy/tree/blast_datatypes
https://github.com/galaxyproject/galaxy/pull/2696

The Galaxy TravisCI tests looked fine.

Peter

On Mon, Aug 1, 2016 at 11:18 AM, Peter Cock <[hidden email]> wrote:

> Dear all,
>
> I ran this past the IUC first, and the only comments were
> positive.
>
> Although I wasn't at GCC2017 to discuss this in person,
> I understand that the Galaxy Team now encourages
> widely used datatypes to be included in the main Galaxy
> repository, rather than distributed via the Tool Shed.
>
> To that end, would a pull request returning the BLAST
> datatypes and associated database *.loc files be welcome?
>
> These are currently on my GitHub repository here:
> https://github.com/peterjc/galaxy_blast/
>
> And the datatypes are distributed via the Tool Shed here:
> http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
>
> Assuming this happens, we would need to phase out the
> tool shed version (but it will still be needed while older
> Galaxy instances are still running).
>
> Are there any pitfalls to worry about if the datatypes are
> already there with Galaxy and the tool shed version is
> installed on top? Or the tool shed version was installed
> but then Galaxy was updated to include the version
> bundled with Galaxy?
>
> Thanks,
>
> Peter
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Re: Returning BLAST datatypes and DB loc files to Galaxy core?

Gildas Le Corguillé
Hi all,

If indeed, datatypes return within the Galaxy distribution, can we imagine propose different datatypes_conf.xml?

Galaxy isn’t anymore dedicated to NGS purpose. It is use also for metabolomics, proteomics, … 

So it could be great to propose 1 "common" list of datatypes (text, tabular, png, pdf, …) and n specific datatypes lists for the n scientific areas to reduce this huge list of datatypes proposed to the users.
Maybe this selection should be based on edam ontology. As you know they are almost already annotated with edam_format and edam_data


Gildas

-----------------------------------------------------------------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
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Le 1 août 2016 à 18:41, Peter Cock <[hidden email]> a écrit :

I have a work-in-progress branch and pull request here,
https://github.com/peterjc/galaxy/tree/blast_datatypes
https://github.com/galaxyproject/galaxy/pull/2696

The Galaxy TravisCI tests looked fine.

Peter

On Mon, Aug 1, 2016 at 11:18 AM, Peter Cock <[hidden email]> wrote:
Dear all,

I ran this past the IUC first, and the only comments were
positive.

Although I wasn't at GCC2017 to discuss this in person,
I understand that the Galaxy Team now encourages
widely used datatypes to be included in the main Galaxy
repository, rather than distributed via the Tool Shed.

To that end, would a pull request returning the BLAST
datatypes and associated database *.loc files be welcome?

These are currently on my GitHub repository here:
https://github.com/peterjc/galaxy_blast/

And the datatypes are distributed via the Tool Shed here:
http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes

Assuming this happens, we would need to phase out the
tool shed version (but it will still be needed while older
Galaxy instances are still running).

Are there any pitfalls to worry about if the datatypes are
already there with Galaxy and the tool shed version is
installed on top? Or the tool shed version was installed
but then Galaxy was updated to include the version
bundled with Galaxy?

Thanks,

Peter
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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 http://galaxyproject.org/search/mailinglists/


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Re: Returning BLAST datatypes and DB loc files to Galaxy core?

Peter Cock
Hi Gildas,

When datatypes were moved to the Tool Shed, I
think the idea was to eventually have only a core
set of topic-neutral datatypes (plain text, tabular,
etc) in Galaxy itself. That does seem sensible.

I'm not quite sure why policy has returned to a
larger centralised set - but limitations of the
ToolShed like dependencies (for Python code
imported directly into Galaxy), lack of versioning
of datatypes, and better control of namespaces
are likely part of this. I missed GCC2017 sadly.

Even with a large set of datatypes included with
Galaxy, it should be easy to hide/disable lots
(e.g. for an image analysis Galaxy you would
not want any of the sequence file formats).

Peter

P.S. Good point about EDAM, its been raised
on the BLAST datatypes pull request:
https://github.com/galaxyproject/galaxy/pull/2696


On Mon, Aug 1, 2016 at 9:27 PM, Gildas Le Corguillé
<[hidden email]> wrote:

> Hi all,
>
> If indeed, datatypes return within the Galaxy distribution, can we imagine
> propose different datatypes_conf.xml?
>
> Galaxy isn’t anymore dedicated to NGS purpose. It is use also for
> metabolomics, proteomics, …
>
> So it could be great to propose 1 "common" list of datatypes (text, tabular,
> png, pdf, …) and n specific datatypes lists for the n scientific areas to
> reduce this huge list of datatypes proposed to the users.
> Maybe this selection should be based on edam ontology. As you know they are
> almost already annotated with edam_format and edam_data
>
>
> Gildas
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/