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:
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(a)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.
On Mon May 23 09:29:35 2016, jmchilton(a)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
On Sun, May 22, 2016 at 7:17 AM, Björn Grüning
> Hi George,
> how do you start your container? Anything special in your network
> I can not reproduce this with 16.04 and 16.01 and have never seen
> Which version of Docker? Is this under Linux?
> I'm a little bit puzzled here.
>> Hi Bjorn,
>> We are using https://hub.docker.com/r/bgruening/galaxy-stable/
>> *To summarize the problem:*
>> We are migrating our Production Galaxy (
) to a *Docker*
>> When you submit a job, the */screen does not refresh/*, you have
>> 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
>> Platform, as our Users are not accustomed to press F5 to refresh
>> Can you look into that?
>> 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(a)gmail.com <mailto:firstname.lastname@example.org>>
>> Hi George,
>> are you using this Docker container?
>> If so which version? I haven't seen this behaviour so far.
>> Am 14.04.2016 um 08:04 schrieb George Weingart:
>> > Hello,
>> > We are installing Galaxy in a Docker environment and we are
>> > 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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