problem with Visualization 'Scatterplot' in 18.05

classic Classic list List threaded Threaded
5 messages Options
| Threaded
Open this post in threaded view
|

problem with Visualization 'Scatterplot' in 18.05

Hans-Rudolf Hotz
Hi all


I am in the process of upgrading our servers to 18.05. And I have
encountered an issue with the Visualization tool "Scatterplot, Creates a
2D-scatterplot from tabular datapoints"

I am starting with a simple bed file for chromosome 15 (downloaded with
UCSC table browser tool). When I click on the Visualization icon,
followed by "Scatterplot", I end up with an near empty page. I only get
the title:

Scatterplot of 'UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)'

UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)



This happens with our development server (after being upgraded from
17.09). It is the same using a new clone of 18.05 code.

It also happens on usegalaxy.eu but it does work on usegalaxy.org


As a side note: on usegalaxy.org, each visualization has its little icon
(see: 'usegalaxy.org.png'), while on usegalaxy.eu, each visualization
just has an eye (see: 'usegalaxy.eu.png')


I hope there is an easy fix for this....


Regards, Hans-Rudolf


--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland

___________________________________________________________
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/

usegalaxy.org.png (10K) Download Attachment
usegalaxy.eu.png (7K) Download Attachment
| Threaded
Open this post in threaded view
|

Re: problem with Visualization 'Scatterplot' in 18.05

Hans-Rudolf Hotz

just adding a little bit more information:

  - this problem happens independent of using paste or uwsgi

  - as far as I have tested all visualization plugins (with the
exception of trackster) are broken. For broken visualizations, other
than 'scatterplot', I get the error: "Load function 'load' not found"


Regards,
Hans-Rudolf


On 06/05/2018 05:14 PM, Hans-Rudolf Hotz wrote:

> Hi all
>
>
> I am in the process of upgrading our servers to 18.05. And I have
> encountered an issue with the Visualization tool "Scatterplot, Creates a
> 2D-scatterplot from tabular datapoints"
>
> I am starting with a simple bed file for chromosome 15 (downloaded with
> UCSC table browser tool). When I click on the Visualization icon,
> followed by "Scatterplot", I end up with an near empty page. I only get
> the title:
>
> Scatterplot of 'UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)'
>
> UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)
>
>
>
> This happens with our development server (after being upgraded from
> 17.09). It is the same using a new clone of 18.05 code.
>
> It also happens on usegalaxy.eu but it does work on usegalaxy.org
>
>
> As a side note: on usegalaxy.org, each visualization has its little icon
> (see: 'usegalaxy.org.png'), while on usegalaxy.eu, each visualization
> just has an eye (see: 'usegalaxy.eu.png')
>
>
> I hope there is an easy fix for this....
>
>
> Regards, Hans-Rudolf
>
>
>
>
> ___________________________________________________________
> 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/
| Threaded
Open this post in threaded view
|

Re: problem with Visualization 'Scatterplot' in 18.05

Nicola Soranzo-3
Dear Hans-Rudolf,
I think this is being worked on at
https://github.com/galaxyproject/galaxy/pull/6297 .

Cheers,
Nicola

On 08/06/18 14:57, Hans-Rudolf Hotz wrote:

>
> just adding a little bit more information:
>
>  - this problem happens independent of using paste or uwsgi
>
>  - as far as I have tested all visualization plugins (with the
> exception of trackster) are broken. For broken visualizations, other
> than 'scatterplot', I get the error: "Load function 'load' not found"
>
>
> Regards,
> Hans-Rudolf
>
>
> On 06/05/2018 05:14 PM, Hans-Rudolf Hotz wrote:
>> Hi all
>>
>>
>> I am in the process of upgrading our servers to 18.05. And I have
>> encountered an issue with the Visualization tool "Scatterplot, Creates a
>> 2D-scatterplot from tabular datapoints"
>>
>> I am starting with a simple bed file for chromosome 15 (downloaded with
>> UCSC table browser tool). When I click on the Visualization icon,
>> followed by "Scatterplot", I end up with an near empty page. I only get
>> the title:
>>
>> Scatterplot of 'UCSC Main on Human: ncbiRefSeq
>> (chr15:20010162-22868384)'
>>
>> UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)
>>
>>
>>
>> This happens with our development server (after being upgraded from
>> 17.09). It is the same using a new clone of 18.05 code.
>>
>> It also happens on usegalaxy.eu but it does work on usegalaxy.org
>>
>>
>> As a side note: on usegalaxy.org, each visualization has its little icon
>> (see: 'usegalaxy.org.png'), while on usegalaxy.eu, each visualization
>> just has an eye (see: 'usegalaxy.eu.png')
>>
>>
>> I hope there is an easy fix for this....
>>
>>
>> Regards, Hans-Rudolf
>>
>>
>>
>>
>> ___________________________________________________________
>> 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/

___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: problem with Visualization 'Scatterplot' in 18.05

Martin Čech
Hi Hans-Rudolf,

the problem is that the 18.05 release is missing the viz static files in the proper folder. To be precise /config/plugins/visualizations/*/static needs to be copied to /static/plugins/visualizations/*/static

To fix:

(make sure you have node 8.x.x and not newer)

$ cd client
$ ./node_modules/.bin/gulp plugins

I am sorry for the inconvenience, we will fix this in the release branch early next week.

Martin







On Fri, Jun 8, 2018 at 10:00 AM Nicola Soranzo <[hidden email]> wrote:
Dear Hans-Rudolf,
I think this is being worked on at
https://github.com/galaxyproject/galaxy/pull/6297 .

Cheers,
Nicola

On 08/06/18 14:57, Hans-Rudolf Hotz wrote:
>
> just adding a little bit more information:
>
>  - this problem happens independent of using paste or uwsgi
>
>  - as far as I have tested all visualization plugins (with the
> exception of trackster) are broken. For broken visualizations, other
> than 'scatterplot', I get the error: "Load function 'load' not found"
>
>
> Regards,
> Hans-Rudolf
>
>
> On 06/05/2018 05:14 PM, Hans-Rudolf Hotz wrote:
>> Hi all
>>
>>
>> I am in the process of upgrading our servers to 18.05. And I have
>> encountered an issue with the Visualization tool "Scatterplot, Creates a
>> 2D-scatterplot from tabular datapoints"
>>
>> I am starting with a simple bed file for chromosome 15 (downloaded with
>> UCSC table browser tool). When I click on the Visualization icon,
>> followed by "Scatterplot", I end up with an near empty page. I only get
>> the title:
>>
>> Scatterplot of 'UCSC Main on Human: ncbiRefSeq
>> (chr15:20010162-22868384)'
>>
>> UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)
>>
>>
>>
>> This happens with our development server (after being upgraded from
>> 17.09). It is the same using a new clone of 18.05 code.
>>
>> It also happens on usegalaxy.eu but it does work on usegalaxy.org
>>
>>
>> As a side note: on usegalaxy.org, each visualization has its little icon
>> (see: 'usegalaxy.org.png'), while on usegalaxy.eu, each visualization
>> just has an eye (see: 'usegalaxy.eu.png')
>>
>>
>> I hope there is an easy fix for this....
>>
>>
>> Regards, Hans-Rudolf
>>
>>
>>
>>
>> ___________________________________________________________
>> 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/

___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: problem with Visualization 'Scatterplot' in 18.05

Hans-Rudolf Hotz
Dear Martin and Nicola

Thank you very much for your help

Unfortunately, I don't have node....but manually copying the files seems
to do the trick.


Regards, Hans-Rudolf



On 06/08/2018 04:48 PM, Martin Čech wrote:

> Hi Hans-Rudolf,
>
> the problem is that the 18.05 release is missing the viz static files in
> the proper folder. To be precise /config/plugins/visualizations/*/static
> needs to be copied to /static/plugins/visualizations/*/static
>
> To fix:
>
> (make sure you have node 8.x.x and not newer)
>
> $ cd client
> $ ./node_modules/.bin/gulp plugins
>
> I am sorry for the inconvenience, we will fix this in the release branch
> early next week.
>
> Martin
>
>
>
>
>
>
>
> On Fri, Jun 8, 2018 at 10:00 AM Nicola Soranzo <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Dear Hans-Rudolf,
>     I think this is being worked on at
>     https://github.com/galaxyproject/galaxy/pull/6297 .
>
>     Cheers,
>     Nicola
>
>     On 08/06/18 14:57, Hans-Rudolf Hotz wrote:
>      >
>      > just adding a little bit more information:
>      >
>      >  - this problem happens independent of using paste or uwsgi
>      >
>      >  - as far as I have tested all visualization plugins (with the
>      > exception of trackster) are broken. For broken visualizations, other
>      > than 'scatterplot', I get the error: "Load function 'load' not found"
>      >
>      >
>      > Regards,
>      > Hans-Rudolf
>      >
>      >
>      > On 06/05/2018 05:14 PM, Hans-Rudolf Hotz wrote:
>      >> Hi all
>      >>
>      >>
>      >> I am in the process of upgrading our servers to 18.05. And I have
>      >> encountered an issue with the Visualization tool "Scatterplot,
>     Creates a
>      >> 2D-scatterplot from tabular datapoints"
>      >>
>      >> I am starting with a simple bed file for chromosome 15
>     (downloaded with
>      >> UCSC table browser tool). When I click on the Visualization icon,
>      >> followed by "Scatterplot", I end up with an near empty page. I
>     only get
>      >> the title:
>      >>
>      >> Scatterplot of 'UCSC Main on Human: ncbiRefSeq
>      >> (chr15:20010162-22868384)'
>      >>
>      >> UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)
>      >>
>      >>
>      >>
>      >> This happens with our development server (after being upgraded from
>      >> 17.09). It is the same using a new clone of 18.05 code.
>      >>
>      >> It also happens on usegalaxy.eu <http://usegalaxy.eu> but it
>     does work on usegalaxy.org <http://usegalaxy.org>
>      >>
>      >>
>      >> As a side note: on usegalaxy.org <http://usegalaxy.org>, each
>     visualization has its little icon
>      >> (see: 'usegalaxy.org.png'), while on usegalaxy.eu
>     <http://usegalaxy.eu>, each visualization
>      >> just has an eye (see: 'usegalaxy.eu.png')
>      >>
>      >>
>      >> I hope there is an easy fix for this....
>      >>
>      >>
>      >> Regards, Hans-Rudolf
>      >>
>      >>
>      >>
>      >>
>      >> ___________________________________________________________
>      >> 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/
>
>     ___________________________________________________________
>     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/