unipept visualization

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unipept visualization

Matthias Bernt
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,
[hidden email], 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:
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Re: unipept visualization

Aysam Guerler
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 <[hidden email]> 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 <a href="tel:%2B49%20341%20235%20482296" value="+49341235482296" target="_blank">+49 341 235 482296,
[hidden email], 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/


___________________________________________________________
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/
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Re: unipept visualization

Matthias Bernt
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 <[hidden email]
> <mailto:[hidden email]>> 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>,
>     [hidden email] <mailto:[hidden email]>, 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,
[hidden email], 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/
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Re: unipept visualization

Aysam Guerler
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:

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 <[hidden email]> 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 <a href="tel:25.08.2017%2019" value="+12508201719" target="_blank">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 <[hidden email] <mailto:[hidden email]>> 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 <a href="tel:%2B49%20341%20235%20482296" value="+49341235482296" target="_blank">+49 341 235 482296 <tel:%2B49%20341%20235%20482296>,
    [hidden email] <mailto:[hidden email]>, 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 <a href="tel:%2B49%20341%20235%20482296" value="+49341235482296" target="_blank">+49 341 235 482296,
[hidden email], 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/
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Re: unipept visualization

Matthias Bernt
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 <[hidden email]
> <mailto:[hidden email]>> 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 <[hidden email]
>         <mailto:[hidden email]> <mailto:[hidden email]
>         <mailto:[hidden email]>>> 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>,
>         [hidden email] <mailto:[hidden email]> <mailto:[hidden email]
>         <mailto:[hidden email]>>, 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>,
>     [hidden email] <mailto:[hidden email]>, 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,
[hidden email], 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/
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Re: unipept visualization

Nicola Soranzo-2
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 <[hidden email]
>> <mailto:[hidden email]>> 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 <[hidden email]
>>         <mailto:[hidden email]> <mailto:[hidden email]
>>         <mailto:[hidden email]>>> 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>,
>>         [hidden email] <mailto:[hidden email]> <mailto:[hidden email]
>>         <mailto:[hidden email]>>, 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>,
>>     [hidden email] <mailto:[hidden email]>, 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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Re: unipept visualization

Matthias Bernt
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 <[hidden email]
>>> <mailto:[hidden email]>> 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 <[hidden email]
>>>         <mailto:[hidden email]> <mailto:[hidden email]
>>>         <mailto:[hidden email]>>> 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>,
>>>         [hidden email] <mailto:[hidden email]> <mailto:[hidden email]
>>>         <mailto:[hidden email]>>, 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>,
>>>     [hidden email] <mailto:[hidden email]>, 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,
[hidden email], 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:
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Re: unipept visualization

Nicola Soranzo-2
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 <[hidden email]
>>>> <mailto:[hidden email]>> 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
>>>> <[hidden email]
>>>>         <mailto:[hidden email]> <mailto:[hidden email]
>>>>         <mailto:[hidden email]>>> 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>,
>>>>         [hidden email] <mailto:[hidden email]> <mailto:[hidden email]
>>>>         <mailto:[hidden email]>>, 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>,
>>>>     [hidden email] <mailto:[hidden email]>, 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/

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