By "generic", I mean just following the commands in the documentation without any deviation. MySQL is installed and run from within the docker container. We don't need this, as we already have a MariaDB server running locally.
We have a lot of users with custom tracks in our local MariaDB server, and so I hope the Docker version can maintain these. I believe it is possible to modify the hg.conf file within the Docker container after the fact, but I haven't gotten that far yet. The Docker image is quite large (~8GB), and so we've needed to create a large VM to handle it.
Does the browser installation procedure in the Dockerfile simply download pre-built executables, or does it compile anything?
David
On 1/29/2024 10:49 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> Hi David,
> The docker procedure is current, I think. What do you mean with "generic"? The Unix commands are rather specific:
>
https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <
https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>
> Can you elaborate what you mean with "accommodate our local mirror" ?
>
> I just tried an Ubuntu 22 a few days ago and ran the browserSetup.sh script in it and it just worked. I didn't use the docker commands, ran the browserSetup.sh -b install manually but I had a working mirror 2 minutes later.
>
> I wanted to try Rocky 8 next and unfortunately got distracted by grant reviews...
>
>
>
> On Mon, Jan 29, 2024 at 3:38 PM Hoover, David (NIH/CIT) [E] <
hoov...@hpc.nih.gov <mailto:
hoov...@hpc.nih.gov>> wrote:
>
> How up to date is the Docker procedure for the Genome Browser? How difficult would it be to create and use a docker image of the Genome Browser that does not have mysql running internally? We have a substantial mariadb server already full with UCSC data and constantly updated, as well as lots of users' custom tracks. The instructions at
https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <
https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> are very generic and would need to be elaborated to accommodate our local mirror.
>
> David
>
> On 1/22/2024 2:44 PM, Christopher Lee wrote:
> > Hi Belinda and David,
> >
> > Unfortunately we are just completely stumped on what is going on here,
> > and we do not have the resources to continue looking further. The only
> > thing we can say is that we ourselves are upgrading to Rocky 9 soon
> > and have verified at least minimal function with that operating
> > system, so you can try upgrading and see if that fixes the problem.
> >
> > As far as theories, we suspect that somehow the MySQL/MariaDb
> > installation could be misconfigured, even though that seemed to have
> > been ruled out already.
> >
> > If you do find the cause of the problem and/or a fix, we would of
> > course love to hear about it and accept a pull request or fix.
> >
> > Thanks,
> > Christopher Lee
> > UCSC Genomics Institute
> >
> > On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
> > <
giar...@bx.psu.edu <mailto:
giar...@bx.psu.edu>> wrote:
> >>
> >> I put a copy of the files in the cgi-bin here
> >>
https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <
https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/>
> >>
> >> If you mean you want to be able to access the pages on our server the
> >> public version is
> >>
https://main.genome-browser.bx.psu.edu/ <
https://main.genome-browser.bx.psu.edu/>
> >>
> >> Belinda
> >>
> >>
> >> On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> >>
> >>> Hello,
> >>>
> >>> Thank you for using the UCSC Genome Browser and reporting your issues.
> >>>
> >>> Would it be possible to place the binaries in a web-accessible location?
> >>> This way, our engineers can have a reproducible case to debug the issue.
> >>>
> >>> If you have any further questions, please reply to
gen...@soe.ucsc.edu <mailto:
gen...@soe.ucsc.edu>.
> >>> All messages sent to that address are archived on a publicly accessible
> >>> Google Groups forum.
> >>> If your question includes sensitive data, you may send it instead to
> >>>
genom...@soe.ucsc.edu <mailto:
genom...@soe.ucsc.edu>.
> >>>
> >>> Jairo Navarro
> >>> UCSC Genome Browser
> >>>
> >>> On Tue, Jan 2, 2024 at 8:56?AM Belinda M. Giardine <
giar...@bx.psu.edu <mailto:
giar...@bx.psu.edu>>
> >>> wrote:
> >>>
> >>>> We are building our own binaries. It is running on a VM.
> >>>>
> >>>> Belinda
> >>>>
> >>>>
> >>>> On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> >>>>
> >>>>> David and Belinda,
> >>>>> thank you for your patience with this, it's hard to debug if we don't
> >>>> have
> >>>>> access to a machine and can't reproduce the problem. We don't think it's
> >>>>> Rocky 9 itself (trying with a VM).
> >>>>> Are you both building your own binaries from the source code or are you
> >>>>> using our pre-built binaries?
> >>>>> thanks
> >>>>> Max
> >>>>>
> >>>>> On Mon, Dec 18, 2023 at 8:31?PM Belinda M. Giardine <
giar...@bx.psu.edu <mailto:
giar...@bx.psu.edu>
> >>>>>>
genome.ucsc.edu <
http://genome.ucsc.edu>
> >>>>>>>>>>> Genome Browser Mirror-Specific Support <
genome...@soe.ucsc.edu <mailto:
genome...@soe.ucsc.edu>
> >>>>>
> >>>>>>>>>>> wrote:
> >>>>>>>>>>>>
> >>>>>>>>>>>> Now I am not so sure what is happening.? Here are some
> >>>> observations:
> >>>>>>>>>>>>
> >>>>>>>>>>>> * The timeout issue holds not just for custom tracks, for the
> >>>> track
> >>>>>>>>>>>> hubs as well
> >>>>>>>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our
> >>>> local
> >>>>>>>>>>>> dataserver (
hpc.nih.gov <
http://hpc.nih.gov>), and these display normally
> >>>>>>>>>>>> Email:
hoov...@hpc.nih.gov <mailto:
hoov...@hpc.nih.gov>
> >>>>>>>>>>>>
> >>>>>>>>>>>> --
> >>>>>>>>>>>>
> >>>>>>>>>>>> ---
> >>>>>>>>>>>> You received this message because you are subscribed to the Google
> >>>>>>>>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> >>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> >>>>>> send
> >>>>>>>>>>>> an email to
genome-mirro...@soe.ucsc.edu <mailto:
genome-mirror%2Bunsu...@soe.ucsc.edu>.
> >>>>>>>>>>>> To view this discussion on the web visit
> >>>>>>>>>>>>
> >>>>>>
> >>>>
https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <
https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>
> >>>>>> .
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>> David Hoover, Ph.D.
> >>>>>>>>> Computational Biologist
> >>>>>>>>> High Performance Computing Services,
> >>>>>>>>> Center for Information Technology,
> >>>>>>>>> National Institutes of Health
> >>>>>>>>> 12 South Dr., Rm 2N207
> >>>>>>>>> Bethesda, MD 20892, USA
> >>>>>>>>> TEL:
(+1) 301-435-2986
> >>>>>>>>> Email:
hoov...@hpc.nih.gov <mailto:
hoov...@hpc.nih.gov>
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>>
> >>>>>>>>> ---
> >>>>>>>>> You received this message because you are subscribed to the Google
> >>>>>> Groups
> >>>>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> >>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> >>>> send
> >>>>>> an
> >>>>>>>>> email to
genome-mirro...@soe.ucsc.edu <mailto:
genome-mirror%2Bunsu...@soe.ucsc.edu>.
> >>>>>>>>> To view this discussion on the web visit
> >>>>>>>>>
> >>>>>>
> >>>>
https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <
https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>
> >>>>>> .
> >>>>>>>
> >>>>>>> --
> >>>>>>> David Hoover, Ph.D.
> >>>>>>> Computational Biologist
> >>>>>>> High Performance Computing Services,
> >>>>>>> Center for Information Technology,
> >>>>>>> National Institutes of Health
> >>>>>>> 12 South Dr., Rm 2N207
> >>>>>>> Bethesda, MD 20892, USA
> >>>>>>> TEL:
(+1) 301-435-2986
> >>>>>>> Email:
hoov...@hpc.nih.gov <mailto:
hoov...@hpc.nih.gov>
> >>>>>>>
> >>>>>>> --
> >>>>>>>
> >>>>>>> --- You received this message because you are subscribed to the Google
> >>>>>> Groups
> >>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> >>>>>>> To unsubscribe from this group and stop receiving emails from it, send
> >>>>>> an
> >>>>>>> email to
genome-mirro...@soe.ucsc.edu <mailto:
genome-mirror%2Bunsu...@soe.ucsc.edu>.
> >>>>>>> To view this discussion on the web visit
> >>>>>>>
> >>>>>>
> >>>>
https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <
https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>
> >>>>>> .
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>> --
> >>>>>>
> >>>>>> ---
> >>>>>> You received this message because you are subscribed to the Google
> >>>> Groups
> >>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> >>>>>> To unsubscribe from this group and stop receiving emails from it, send
> >>>> an
> >>>>>> email to
genome-mirro...@soe.ucsc.edu <mailto:
genome-mirror%2Bunsu...@soe.ucsc.edu>.
> >>>>>> To view this discussion on the web visit
> >>>>>>
> >>>>
https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <
https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>
> >>>>>> .
> >>>>>>
> >>>>>
> >>>>
> >>>> --
> >>>>
> >>>> ---
> >>>> You received this message because you are subscribed to the Google Groups
> >>>> "UCSC Genome Browser Mirror-Specific Support" group.
> >>>> To unsubscribe from this group and stop receiving emails from it, send an
> >>>> email to
genome-mirro...@soe.ucsc.edu <mailto:
genome-mirror%2Bunsu...@soe.ucsc.edu>.
> >>>> To view this discussion on the web visit
> >>>>
https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <
https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu>
> >>>> .
> >>>>
> >>>
>
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL:
(+1) 301-435-2986
> Email:
hoov...@hpc.nih.gov <mailto:
hoov...@hpc.nih.gov>
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to
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> To view this discussion on the web visit
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