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, m.bernt@ufz.de, 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 -------------------------------------------
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.bernt@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 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, m.bernt@ufz.de, 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 ------------------------------------------- ___________________________________________________________ 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/
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 19:05, 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.bernt@ufz.de <mailto:m.bernt@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 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.bernt@ufz.de <mailto:m.bernt@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 ------------------------------------------- ___________________________________________________________ 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/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/>
-- ------------------------------------------- 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, m.bernt@ufz.de, 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 -------------------------------------------
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/visualizatio... . 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.bernt@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 19:05, 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.bernt@ufz.de <mailto: m.bernt@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 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.bernt@ufz.de <mailto:m.bernt@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 ------------------------------------------- ___________________________________________________________ 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/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/>
--
------------------------------------------- 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, m.bernt@ufz.de, 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 -------------------------------------------
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/visualizatio....
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.bernt@ufz.de <mailto:m.bernt@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.bernt@ufz.de <mailto:m.bernt@ufz.de> <mailto:m.bernt@ufz.de <mailto:m.bernt@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 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>, m.bernt@ufz.de <mailto:m.bernt@ufz.de> <mailto:m.bernt@ufz.de <mailto:m.bernt@ufz.de>>, www.ufz.de <http://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 ------------------------------------------- ___________________________________________________________ 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/ <https://lists.galaxyproject.org/> <https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/> <http://galaxyproject.org/search/ <http://galaxyproject.org/search/>>
--
------------------------------------------- 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.bernt@ufz.de <mailto:m.bernt@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 -------------------------------------------
-- ------------------------------------------- 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, m.bernt@ufz.de, 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 -------------------------------------------
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/visualizatio....
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.bernt@ufz.de <mailto:m.bernt@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.bernt@ufz.de <mailto:m.bernt@ufz.de> <mailto:m.bernt@ufz.de <mailto:m.bernt@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 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>, m.bernt@ufz.de <mailto:m.bernt@ufz.de> <mailto:m.bernt@ufz.de <mailto:m.bernt@ufz.de>>, www.ufz.de <http://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 ------------------------------------------- ___________________________________________________________ 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/ <https://lists.galaxyproject.org/> <https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/> <http://galaxyproject.org/search/ <http://galaxyproject.org/search/>>
-- ------------------------------------------- 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.bernt@ufz.de <mailto:m.bernt@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 -------------------------------------------
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/visualizatio....
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.bernt@ufz.de <mailto:m.bernt@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.bernt@ufz.de <mailto:m.bernt@ufz.de> <mailto:m.bernt@ufz.de <mailto:m.bernt@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 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>, m.bernt@ufz.de <mailto:m.bernt@ufz.de> <mailto:m.bernt@ufz.de <mailto:m.bernt@ufz.de>>, www.ufz.de <http://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 ------------------------------------------- ___________________________________________________________ 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/ <https://lists.galaxyproject.org/> <https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/> <http://galaxyproject.org/search/ <http://galaxyproject.org/search/>>
-- ------------------------------------------- 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.bernt@ufz.de <mailto:m.bernt@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 -------------------------------------------
-- ------------------------------------------- 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, m.bernt@ufz.de, 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 -------------------------------------------
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/visualizatio....
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.bernt@ufz.de <mailto:m.bernt@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.bernt@ufz.de <mailto:m.bernt@ufz.de> <mailto:m.bernt@ufz.de <mailto:m.bernt@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.
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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.bernt@ufz.de <mailto:m.bernt@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 -------------------------------------------
participants (3)
-
Aysam Guerler -
Matthias Bernt -
Nicola Soranzo