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 <[email protected]
<mailto:[email protected]>> 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 <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>> 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
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>
<tel:%2B49%20341%20235%20482296>,
[email protected] <mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>, www.ufz.de <http://www.ufz.de>
<http://www.ufz.de>
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Vorsitzender des Aufsichtsrats/Chairman of the Supervisory
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Director:
Prof. Dr. Dr. h.c. Georg Teutsch
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Director:
Prof. Dr. Heike Graßmann
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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>,
[email protected] <mailto:[email protected]>, 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
-------------------------------------------
--
-------------------------------------------
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,
[email protected], 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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