Re: [galaxy-dev] unipept visualization

Fri, 01 Sep 2017 10:01:10 -0700 

Hi Matthias,
the fix is available only on dev at the moment. Please check that if you have a config/datatypes_conf.xml file, this will take precedence over config/datatypes_conf.xml.sample (where the fix was applied), so you may need to merge the changes to config/datatypes_conf.xml (or remove the latter if it doesn't contain useful modifications). 


Also, the visualisation is available only if you are logged in (and it 
works for me when the correct d3_hierarchy datatype is assigned to the 
dataset).


Cheers,
Nicola

On 01/09/17 17:31, Matthias Bernt wrote:

Hi Nicola,

thanks for the info. I tested with the latest dev and a recent 17.05.


Choosing d3_hierarchy at upload does not work, it is not among the 
available options.



Furthermore, I have the problem that galaxy tells me that there is no 
suitable visualization even if I choose the correct data type.


Best,
Matthias

On 31.08.2017 17:39, Nicola Soranzo wrote:

Hi Matthias,

that should be fixed on dev already by pull request: 
https://github.com/galaxyproject/galaxy/pull/4522


Cheers,
Nicola

On 31/08/17 16:30, Matthias Bernt wrote:

Hi Sam,


I tried on 17.05 and dev without any success. Any idea where I could 
start debugging?


Best,
Matthias

On 30.08.2017 18:23, Aysam Guerler wrote:

Hey Matthias,


I noticed that this visualization has already been added and should 
be working in release 17.05 and a d3_hierarchy file. Its documented 
at 
https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/visualizations/unipept. 



Example files are available here:

https://github.com/unipept/unipept-visualizations/tree/master/examples/data 




Now here is the issue I noticed, once you upload one of these 
example files, you need to select the file in the history, click on 
the pencil icon and change the datatype to 'd3_hierarchy' before 
attempting to visualize it. You cannot select the correct datatype 
in the upload view. I will test this a little bit more and fix it 
if necessary for the next release.


I hope this helps.
Thanks again.


On Mon, Aug 28, 2017 at 4:23 AM, Matthias Bernt <m.be...@ufz.de 
<mailto:m.be...@ufz.de>> wrote:


    Hi Sam,


    thanks for the answer. So far I have not configured anything, I 
was

    hoping that it works out of the box :).


    Could you point me to some documentation where the setup is 
explained?


    Best,
    Matthias

    On 25.08.2017 19 <tel:25.08.2017%2019>:05, Aysam Guerler wrote:

        Hi Matthias,


        Have you added the visulization to Charts or the regular 
Galaxy

        visualization framework? If it is the latter please make sure

        that you correctly specified the datatype in your XML file. 
Your

        visualization should than appear in the drop-down list in the
        history.

        Thanks,
        Sam


        On Fri, Aug 25, 2017 at 5:25 AM, Matthias Bernt 
<m.be...@ufz.de

        <mailto:m.be...@ufz.de> <mailto:m.be...@ufz.de
        <mailto:m.be...@ufz.de>>> wrote:

             Dear list,

             I can not get the wonderful unipept visualization to work
        on our

             Galaxy instance (a test instance on the dev branch). I 
get

        the message:

             "Unfortunately we could not identify a suitable 
plugin...."


             The file I try to visualize was generated by unipept
        (pept2lca) and
             is of format d3_hierarchy.

             Could someone tell me if I need to install / configure
        something to
             get this running?

             Thanks a lot.

             Best,
             Matthias



             P.S. This might be also of interest for others, since 
this
             visualization is used in the Metaproteomics tutorial 
of the

        GTN.


             --
             -------------------------------------------
             Matthias Bernt
             Bioinformatics Service
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    --
    -------------------------------------------
    Matthias Bernt
    Bioinformatics Service
    Molekulare Systembiologie (MOLSYB)
    Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
    Helmholtz Centre for Environmental Research GmbH - UFZ
    Permoserstraße 15, 04318 Leipzig, Germany
    Phone +49 341 235 482296 <tel:%2B49%20341%20235%20482296>,

    m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de 
<http://www.ufz.de>


    Sitz der Gesellschaft/Registered Office: Leipzig
    Registergericht/Registration Office: Amtsgericht Leipzig
    Handelsregister Nr./Trade Register Nr.: B 4703
    Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
    MinDirig Wilfried Kraus
    Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
    Prof. Dr. Dr. h.c. Georg Teutsch

    Administrative Geschäftsführerin/ Administrative Managing 
Director:

    Prof. Dr. Heike Graßmann
    -------------------------------------------










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