Refresh of screens in Galaxy Docker environment
Hello, We are installing Galaxy in a Docker environment and we are encountering an issue where we need to refresh the screen (For Example, using F5) in order to see the status of the job. We see that using chrome as browser. If we don't refresh the screen, it stays (The job might have completed long ago but it still shows executing in yellow) Any suggestions how to resolve the problem? Thanks! George Weingart
Hi George, are you using this Docker container? https://github.com/bgruening/docker-galaxy-stable If so which version? I haven't seen this behaviour so far. Ciao, Bjoern Am 14.04.2016 um 08:04 schrieb George Weingart:
Hello,
We are installing Galaxy in a Docker environment and we are encountering an issue where we need to refresh the screen (For Example, using F5) in order to see the status of the job. We see that using chrome as browser. If we don't refresh the screen, it stays (The job might have completed long ago but it still shows executing in yellow)
Any suggestions how to resolve the problem?
Thanks! George Weingart
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Hi Bjorn, We are using https://hub.docker.com/r/bgruening/galaxy-stable/ *To summarize the problem:* We are migrating our Production Galaxy ( http://huttenhower.sph.harvard.edu/galaxy/) to a *Docker* environment. When you submit a job, the *screen does not refresh*, you have to hit *F5* to refresh the screens. I verified the problem occurs *both *when we use *Chrome and IE* It is a severe problem, that could impact deployment to our new Docker Platform, as our Users are not accustomed to press F5 to refresh the screen. Can you look into that? Thanks! George Weingart PhD Huttenhower Lab Harvard School of Public Health *Before F5 pressed* [image: Inline image 1] *After F5 pressed.* [image: Inline image 2] On Wed, Apr 13, 2016 at 11:10 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi George,
are you using this Docker container?
https://github.com/bgruening/docker-galaxy-stable
If so which version? I haven't seen this behaviour so far.
Ciao, Bjoern
Am 14.04.2016 um 08:04 schrieb George Weingart:
Hello,
We are installing Galaxy in a Docker environment and we are encountering an issue where we need to refresh the screen (For Example, using F5) in order to see the status of the job. We see that using chrome as browser. If we don't refresh the screen, it stays (The job might have completed long ago but it still shows executing in yellow)
Any suggestions how to resolve the problem?
Thanks! George Weingart
___________________________________________________________ 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/mailinglists/
Hi, this sounds strange :( I will look at it asap. In the meantime can you please try this image: https://quay.io/repository/bgruening/galaxy Especially the 16.04 release. Dockerhub is completely unreliable for me in the last month and quay.io works better for me. Thanks for using Galaxy! Bjoern
Hi Bjorn,
We are using https://hub.docker.com/r/bgruening/galaxy-stable/
*To summarize the problem:*
We are migrating our Production Galaxy ( http://huttenhower.sph.harvard.edu/galaxy/) to a *Docker* environment.
When you submit a job, the */screen does not refresh/*, you have to hit *F5* to refresh the screens. I verified the problem occurs *both *when we use *Chrome and IE* * * It is a severe problem, that could impact deployment to our new Docker Platform, as our Users are not accustomed to press F5 to refresh the screen.
Can you look into that?
Thanks!
George Weingart PhD Huttenhower Lab Harvard School of Public Health
*Before F5 pressed*
Inline image 1
*After F5 pressed.*
Inline image 2
On Wed, Apr 13, 2016 at 11:10 PM, Björn Grüning <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>> wrote:
Hi George,
are you using this Docker container?
https://github.com/bgruening/docker-galaxy-stable
If so which version? I haven't seen this behaviour so far.
Ciao, Bjoern
Am 14.04.2016 um 08:04 schrieb George Weingart: > Hello, > > We are installing Galaxy in a Docker environment and we are encountering > an issue where we need to refresh the screen (For Example, using F5) in > order to see the status of the job. > We see that using chrome as browser. > If we don't refresh the screen, it stays (The job might have completed > long ago but it still shows executing in yellow) > > Any suggestions how to resolve the problem? > > Thanks! > George Weingart > > > > ___________________________________________________________ > 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/mailinglists/ >
Hi George, how do you start your container? Anything special in your network settings. I can not reproduce this with 16.04 and 16.01 and have never seen this before. Which version of Docker? Is this under Linux? I'm a little bit puzzled here. Sorry, Bjoern
Hi Bjorn,
We are using https://hub.docker.com/r/bgruening/galaxy-stable/
*To summarize the problem:*
We are migrating our Production Galaxy ( http://huttenhower.sph.harvard.edu/galaxy/) to a *Docker* environment.
When you submit a job, the */screen does not refresh/*, you have to hit *F5* to refresh the screens. I verified the problem occurs *both *when we use *Chrome and IE* * * It is a severe problem, that could impact deployment to our new Docker Platform, as our Users are not accustomed to press F5 to refresh the screen.
Can you look into that?
Thanks!
George Weingart PhD Huttenhower Lab Harvard School of Public Health
*Before F5 pressed*
Inline image 1
*After F5 pressed.*
Inline image 2
On Wed, Apr 13, 2016 at 11:10 PM, Björn Grüning <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>> wrote:
Hi George,
are you using this Docker container?
https://github.com/bgruening/docker-galaxy-stable
If so which version? I haven't seen this behaviour so far.
Ciao, Bjoern
Am 14.04.2016 um 08:04 schrieb George Weingart: > Hello, > > We are installing Galaxy in a Docker environment and we are encountering > an issue where we need to refresh the screen (For Example, using F5) in > order to see the status of the job. > We see that using chrome as browser. > If we don't refresh the screen, it stays (The job might have completed > long ago but it still shows executing in yellow) > > Any suggestions how to resolve the problem? > > Thanks! > George Weingart > > > > ___________________________________________________________ > 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/mailinglists/ >
It is probably worth looking at this Galaxy issue - this may have little to do with Docker or the Docker server might have a different time configured than a local one? History updating is broken for many clients in 16.04 and I am unsure if this intention is to fix it or not. https://github.com/galaxyproject/galaxy/issues/2242 -John On Sun, May 22, 2016 at 7:17 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi George,
how do you start your container? Anything special in your network settings.
I can not reproduce this with 16.04 and 16.01 and have never seen this before.
Which version of Docker? Is this under Linux? I'm a little bit puzzled here.
Sorry, Bjoern
Hi Bjorn,
We are using https://hub.docker.com/r/bgruening/galaxy-stable/
*To summarize the problem:*
We are migrating our Production Galaxy ( http://huttenhower.sph.harvard.edu/galaxy/) to a *Docker* environment.
When you submit a job, the */screen does not refresh/*, you have to hit *F5* to refresh the screens. I verified the problem occurs *both *when we use *Chrome and IE* * * It is a severe problem, that could impact deployment to our new Docker Platform, as our Users are not accustomed to press F5 to refresh the screen.
Can you look into that?
Thanks!
George Weingart PhD Huttenhower Lab Harvard School of Public Health
*Before F5 pressed*
Inline image 1
*After F5 pressed.*
Inline image 2
On Wed, Apr 13, 2016 at 11:10 PM, Björn Grüning <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>> wrote:
Hi George,
are you using this Docker container?
https://github.com/bgruening/docker-galaxy-stable
If so which version? I haven't seen this behaviour so far.
Ciao, Bjoern
Am 14.04.2016 um 08:04 schrieb George Weingart: > Hello, > > We are installing Galaxy in a Docker environment and we are encountering > an issue where we need to refresh the screen (For Example, using F5) in > order to see the status of the job. > We see that using chrome as browser. > If we don't refresh the screen, it stays (The job might have completed > long ago but it still shows executing in yellow) > > Any suggestions how to resolve the problem? > > Thanks! > George Weingart > > > > ___________________________________________________________ > 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/mailinglists/ >
___________________________________________________________ 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/mailinglists/
All, Just catching up from the thread over the weekend. I put together the galaxy container for the Huttenhower lab and have been working with George. The image is built from bgruening/galaxy-stable:dev. See the repo here: https://github.com/fasrc/fasrc-galaxy We're currently running the "hutlab" branch. The image is pretty big due to a ton of dependencies baked in. The issue George wrote about is related to the number of handlers running. We've been running the container with GALAXY_HANDLER_NUMPROCS=2, and disabling one of the handlers via supervisor seems to "fix" the issue with screen refreshes. Also, please note that if you copy rchelp@fas.harvard.edu, it creates a completely new ticket in our ticketing system. It should be better to use that address in the To: field to preserve the thread on this side. Let us know if you have any questions. Thanks, Nate On Mon May 23 09:29:35 2016, jmchilton@gmail.com wrote:
It is probably worth looking at this Galaxy issue - this may have little to do with Docker or the Docker server might have a different time configured than a local one? History updating is broken for many clients in 16.04 and I am unsure if this intention is to fix it or not.
https://github.com/galaxyproject/galaxy/issues/2242
-John
On Sun, May 22, 2016 at 7:17 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi George,
how do you start your container? Anything special in your network settings.
I can not reproduce this with 16.04 and 16.01 and have never seen this before.
Which version of Docker? Is this under Linux? I'm a little bit puzzled here.
Sorry, Bjoern
Hi Bjorn,
We are using https://hub.docker.com/r/bgruening/galaxy-stable/
*To summarize the problem:*
We are migrating our Production Galaxy ( http://huttenhower.sph.harvard.edu/galaxy/) to a *Docker* environment.
When you submit a job, the */screen does not refresh/*, you have to hit *F5* to refresh the screens. I verified the problem occurs *both *when we use *Chrome and IE* * * It is a severe problem, that could impact deployment to our new Docker Platform, as our Users are not accustomed to press F5 to refresh the screen.
Can you look into that?
Thanks!
George Weingart PhD Huttenhower Lab Harvard School of Public Health
*Before F5 pressed*
Inline image 1
*After F5 pressed.*
Inline image 2
On Wed, Apr 13, 2016 at 11:10 PM, Björn Grüning <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>> wrote:
Hi George,
are you using this Docker container?
https://github.com/bgruening/docker-galaxy-stable
If so which version? I haven't seen this behaviour so far.
Ciao, Bjoern
Am 14.04.2016 um 08:04 schrieb George Weingart: > Hello, > > We are installing Galaxy in a Docker environment and we are encountering > an issue where we need to refresh the screen (For Example, > using F5) in > order to see the status of the job. > We see that using chrome as browser. > If we don't refresh the screen, it stays (The job might have > completed > long ago but it still shows executing in yellow) > > Any suggestions how to resolve the problem? > > Thanks! > George Weingart > > > > ___________________________________________________________ > 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/mailinglists/ >
___________________________________________________________ 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/mailinglists/
participants (4)
-
Björn Grüning -
By Nate St. Germain via RT -
George Weingart -
John Chilton