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

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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
tel: +33 2 98 29 23 81
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Le 1 août 2016 à 18:41, Peter Cock <p.j.a.cock@googlemail.com> 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 <p.j.a.cock@googlemail.com> 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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