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
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/
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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/
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 nicola.soranzo@gmail.com 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/
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 <nicola.soranzo@gmail.com mailto:nicola.soranzo@gmail.com> 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/
galaxy-dev@lists.galaxyproject.org
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Hans-Rudolf Hotz -
Martin Čech -
Nicola Soranzo