problems with Docker generated browser

[Hoover, David (NIH/CIT) [E]]

Hi all,

Something has changed to the browser as of v495. I've built a docker image for v495, v496 and v497 using the same instructions I've used successfully for a while. But since v495, the browser does not display. I can get the gateway page, the tools, and even custom tracks, but the main browser page is just blank. The page source shows the header and a set of javascript sources, but then it just ends prematurely:

> ...
> <script type='text/javascript' SRC='../js/ajax.js?v=1774890328'></script>
> <script type='text/javascript' SRC='../js/jquery.watermarkinput.js?v=1774890328'></script>
> <script type='text/javascript' SRC='../js/jquery.history.js?v=1774890328'></script>
> <script type='text/javascript' SRC='../js/jquery.imgareaselect.js?v=1774890328'></script>
> <script type='text/javascript' SRC='../js/autocomplete.js?v=1774890328'></script>
> <script type='text/javascript' SRC='../js/es5-shim.4.0.3.min.js?v=1774890328'></script>
> <script type='text/javascript' SRC='../js/es5-sham.4.0.3.min.js?v=1774890328'></script>
> <script type='text/javascript' SRC='../js/lodash.3.10.0.compat.min.js?v=1774890328'></script>
> <script type='text/javascript' SRC='../js/aut

I'm not sure what is going on. I've tried pulling the docker file from the master branch as well as the version-specific releases, but it doesn't seem to matter.

Any ideas of what to test?

Thanks,
David

--
David Hoover, Ph.D.
Computational Biologist
CIT SCS HPCS
National Institutes of Health
12 South Dr., Rm 2N207
TEL: (+1) 301-435-2986
Email: david....@nih.gov

[Clay Fischer]

Hi David,

Thanks for reporting this issue.

Our engineering team has shared that while this will be fixed in the next release, a workaround for the time being is to run your docker command with "--shm-size=2g" added, such as:

docker run -d --name gb37466 -p 18080:80 --shm-size=2g genomebrowser/server:latest

You can alternatively ssh into your docker image and change hg.conf to have a line "cacheTrackDbDir=" in it. This should get the browser up.

docker exec -it <id of the image> /bin/bash
echo "cacheTrackDbDir=" >> /usr/local/apache/cgi-bin/hg.conf

Thanks,
Clay Fischer
UCSC Genomics Institute

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